diff --git a/packages/snyk-fix/src/lib/errors/invalid-workspace.ts b/packages/snyk-fix/src/lib/errors/invalid-workspace.ts
new file mode 100644
index 0000000000..6150766d05
--- /dev/null
+++ b/packages/snyk-fix/src/lib/errors/invalid-workspace.ts
@@ -0,0 +1,10 @@
+import { CustomError, ERROR_CODES } from './custom-error';
+
+export class MissingFileNameError extends CustomError {
+  public constructor() {
+    super(
+      'Filename is missing from test result. Please contact support@snyk.io.',
+      ERROR_CODES.MissingFileName,
+    );
+  }
+}
diff --git a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/extract-version-provenance.ts b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/extract-version-provenance.ts
index b75f98d8ee..2b6a61241f 100644
--- a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/extract-version-provenance.ts
+++ b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/extract-version-provenance.ts
@@ -8,7 +8,7 @@ import {
 import { Workspace } from '../../../../types';
 import { containsRequireDirective } from './contains-require-directive';
 
-interface PythonProvenance {
+export interface PythonProvenance {
   [fileName: string]: ParsedRequirements;
 }
 
@@ -20,7 +20,8 @@ export async function extractProvenance(
   fileName: string,
   provenance: PythonProvenance = {},
 ): Promise<PythonProvenance> {
-  const requirementsTxt = await workspace.readFile(path.join(dir, fileName));
+  const requirementsFileName = path.join(dir, fileName);
+  const requirementsTxt = await workspace.readFile(requirementsFileName);
   provenance = {
     ...provenance,
     [fileName]: parseRequirementsFile(requirementsTxt),
diff --git a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/index.ts b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/index.ts
index 2b457a64e7..4467986837 100644
--- a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/index.ts
+++ b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/index.ts
@@ -1,9 +1,14 @@
 import * as debugLib from 'debug';
+import * as pathLib from 'path';
+const sortBy = require('lodash.sortby');
+const groupBy = require('lodash.groupby');
 
 import {
   EntityToFix,
+  FixChangesSummary,
   FixOptions,
-  WithFixChangesApplied,
+  RemediationChanges,
+  Workspace,
 } from '../../../../types';
 import { PluginFixResponse } from '../../../types';
 import { updateDependencies } from './update-dependencies';
@@ -11,7 +16,11 @@ import { MissingRemediationDataError } from '../../../../lib/errors/missing-reme
 import { MissingFileNameError } from '../../../../lib/errors/missing-file-name';
 import { partitionByFixable } from './is-supported';
 import { NoFixesCouldBeAppliedError } from '../../../../lib/errors/no-fixes-applied';
-import { parseRequirementsFile } from './update-dependencies/requirements-file-parser';
+import { extractProvenance } from './extract-version-provenance';
+import {
+  ParsedRequirements,
+  parseRequirementsFile,
+} from './update-dependencies/requirements-file-parser';
 
 const debug = debugLib('snyk-fix:python:requirements.txt');
 
@@ -26,56 +35,207 @@ export async function pipRequirementsTxt(
     skipped: [],
   };
 
-  const { fixable, skipped } = await partitionByFixable(entities);
-  handlerResult.skipped.push(...skipped);
+  const { fixable, skipped: notFixable } = await partitionByFixable(entities);
+  handlerResult.skipped.push(...notFixable);
 
-  for (const entity of fixable) {
-    try {
-      const fixedEntity = await fixIndividualRequirementsTxt(entity, options);
-      handlerResult.succeeded.push(fixedEntity);
-    } catch (e) {
-      handlerResult.failed.push({ original: entity, error: e });
-    }
+  const ordered = sortByDirectory(fixable);
+  const fixedFilesCache: string[] = [];
+  for (const dir of Object.keys(ordered)) {
+    debug(`Fixing entities in directory ${dir}`);
+    const entitiesPerDirectory = ordered[dir].map((e) => e.entity);
+    const { failed, succeeded, skipped, fixedFiles } = await fixAll(
+      entitiesPerDirectory,
+      options,
+      fixedFilesCache,
+    );
+    fixedFilesCache.push(...fixedFiles);
+    handlerResult.succeeded.push(...succeeded);
+    handlerResult.failed.push(...failed);
+    handlerResult.skipped.push(...skipped);
   }
   return handlerResult;
 }
 
-// TODO: optionally verify the deps install
-export async function fixIndividualRequirementsTxt(
+export function getRequiredData(
   entity: EntityToFix,
-  options: FixOptions,
-): Promise<WithFixChangesApplied<EntityToFix>> {
-  const fileName = entity.scanResult.identity.targetFile;
-  const remediationData = entity.testResult.remediation;
-  if (!remediationData) {
+): {
+  remediation: RemediationChanges;
+  targetFile: string;
+  workspace: Workspace;
+} {
+  const { remediation } = entity.testResult;
+  if (!remediation) {
     throw new MissingRemediationDataError();
   }
-  if (!fileName) {
+  const { targetFile } = entity.scanResult.identity;
+  if (!targetFile) {
     throw new MissingFileNameError();
   }
-  const requirementsTxt = await entity.workspace.readFile(fileName);
-  const requirementsData = parseRequirementsFile(requirementsTxt);
+  const { workspace } = entity;
+  if (!workspace) {
+    throw new NoFixesCouldBeAppliedError();
+  }
+  return { targetFile, remediation, workspace };
+}
 
-  // TODO: allow handlers per fix type (later also strategies or combine with strategies)
-  const { updatedManifest, changes } = updateDependencies(
-    requirementsData,
-    remediationData.pin,
+async function fixAll(
+  entities: EntityToFix[],
+  options: FixOptions,
+  fixedCache: string[],
+): Promise<PluginFixResponse & { fixedFiles: string[] }> {
+  const handlerResult: PluginFixResponse = {
+    succeeded: [],
+    failed: [],
+    skipped: [],
+  };
+  for (const entity of entities) {
+    const targetFile = entity.scanResult.identity.targetFile!;
+    try {
+      const { dir, base } = pathLib.parse(targetFile);
+      // parse & join again to support correct separator
+      if (fixedCache.includes(pathLib.join(dir, base))) {
+        handlerResult.succeeded.push({
+          original: entity,
+          changes: [{ success: true, userMessage: 'Previously fixed' }],
+        });
+        continue;
+      }
+      const { changes, fixedFiles } = await applyAllFixes(entity, options);
+      if (!changes.length) {
+        debug('Manifest has not changed!');
+        throw new NoFixesCouldBeAppliedError();
+      }
+      fixedCache.push(...fixedFiles);
+      handlerResult.succeeded.push({ original: entity, changes });
+    } catch (e) {
+      debug(`Failed to fix ${targetFile}.\nERROR: ${e}`);
+      handlerResult.failed.push({ original: entity, error: e });
+    }
+  }
+  return { ...handlerResult, fixedFiles: [] };
+}
+// TODO: optionally verify the deps install
+export async function fixIndividualRequirementsTxt(
+  workspace: Workspace,
+  dir: string,
+  entryFileName: string,
+  fileName: string,
+  remediation: RemediationChanges,
+  parsedRequirements: ParsedRequirements,
+  options: FixOptions,
+  directUpgradesOnly: boolean,
+): Promise<{ changes: FixChangesSummary[]; appliedRemediation: string[] }> {
+  const fullFilePath = pathLib.join(dir, fileName);
+  const { updatedManifest, changes, appliedRemediation } = updateDependencies(
+    parsedRequirements,
+    remediation.pin,
+    directUpgradesOnly,
+    pathLib.join(dir, entryFileName) !== fullFilePath ? fileName : undefined,
   );
 
-  // TODO: do this with the changes now that we only return new
-  if (updatedManifest === requirementsTxt) {
-    debug('Manifest has not changed!');
-    throw new NoFixesCouldBeAppliedError();
+  if (!changes.length) {
+    return { changes, appliedRemediation };
   }
+
   if (!options.dryRun) {
     debug('Writing changes to file');
-    await entity.workspace.writeFile(fileName, updatedManifest);
+    await workspace.writeFile(pathLib.join(dir, fileName), updatedManifest);
   } else {
     debug('Skipping writing changes to file in --dry-run mode');
   }
 
-  return {
-    original: entity,
-    changes,
+  return { changes, appliedRemediation };
+}
+
+export async function applyAllFixes(
+  entity: EntityToFix,
+  options: FixOptions,
+): Promise<{ changes: FixChangesSummary[]; fixedFiles: string[] }> {
+  const { remediation, targetFile: entryFileName, workspace } = getRequiredData(
+    entity,
+  );
+  const fixedFiles: string[] = [];
+  const { dir, base } = pathLib.parse(entryFileName);
+  const provenance = await extractProvenance(workspace, dir, base);
+  const upgradeChanges: FixChangesSummary[] = [];
+  const appliedUpgradeRemediation: string[] = [];
+  /* Apply all upgrades first across all files that are included */
+  for (const fileName of Object.keys(provenance)) {
+    const skipApplyingPins = true;
+    const { changes, appliedRemediation } = await fixIndividualRequirementsTxt(
+      workspace,
+      dir,
+      base,
+      fileName,
+      remediation,
+      provenance[fileName],
+      options,
+      skipApplyingPins,
+    );
+    appliedUpgradeRemediation.push(...appliedRemediation);
+    upgradeChanges.push(...changes);
+    fixedFiles.push(pathLib.join(dir, fileName));
+  }
+
+  /* Apply all left over remediation as pins in the entry targetFile */
+  const requirementsTxt = await workspace.readFile(entryFileName);
+
+  const toPin: RemediationChanges = filterOutAppliedUpgrades(
+    remediation,
+    appliedUpgradeRemediation,
+  );
+  const directUpgradesOnly = false;
+  const { changes: pinnedChanges } = await fixIndividualRequirementsTxt(
+    workspace,
+    dir,
+    base,
+    base,
+    toPin,
+    parseRequirementsFile(requirementsTxt),
+    options,
+    directUpgradesOnly,
+  );
+
+  return { changes: [...upgradeChanges, ...pinnedChanges], fixedFiles };
+}
+
+function filterOutAppliedUpgrades(
+  remediation: RemediationChanges,
+  appliedRemediation: string[],
+): RemediationChanges {
+  const pinRemediation: RemediationChanges = {
+    ...remediation,
+    pin: {}, // delete the pin remediation so we can collect un-applied remediation
   };
+  const pins = remediation.pin;
+  const lowerCasedAppliedRemediation = appliedRemediation.map((i) =>
+    i.toLowerCase(),
+  );
+  for (const pkgAtVersion of Object.keys(pins)) {
+    if (!lowerCasedAppliedRemediation.includes(pkgAtVersion.toLowerCase())) {
+      pinRemediation.pin[pkgAtVersion] = pins[pkgAtVersion];
+    }
+  }
+  return pinRemediation;
+}
+
+function sortByDirectory(
+  entities: EntityToFix[],
+): {
+  [dir: string]: Array<{
+    entity: EntityToFix;
+    dir: string;
+    base: string;
+    ext: string;
+    root: string;
+    name: string;
+  }>;
+} {
+  const mapped = entities.map((e) => ({
+    entity: e,
+    ...pathLib.parse(e.scanResult.identity.targetFile!),
+  }));
+
+  const sorted = sortBy(mapped, 'dir');
+  return groupBy(sorted, 'dir');
 }
diff --git a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/is-supported.ts b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/is-supported.ts
index 25ce4b9cff..35f14f2913 100644
--- a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/is-supported.ts
+++ b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/is-supported.ts
@@ -45,11 +45,13 @@ export async function isSupported(
     };
   }
 
-  const { containsRequire } = await containsRequireDirective(requirementsTxt);
-  if (containsRequire) {
+  const { containsRequire, matches } = await containsRequireDirective(
+    requirementsTxt,
+  );
+  if (containsRequire && matches.some((m) => m.includes('c'))) {
     return {
       supported: false,
-      reason: `Requirements with ${chalk.bold('-r')} or ${chalk.bold(
+      reason: `Requirements with ${chalk.bold(
         '-c',
       )} directive are not yet supported`,
     };
diff --git a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-pins.ts b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-pins.ts
index 779c50a2d8..dc43ee4b2a 100644
--- a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-pins.ts
+++ b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-pins.ts
@@ -6,7 +6,11 @@ import { Requirement } from './requirements-file-parser';
 export function generatePins(
   requirements: Requirement[],
   updates: DependencyPins,
-): { pinnedRequirements: string[]; changes: FixChangesSummary[] } {
+): {
+  pinnedRequirements: string[];
+  changes: FixChangesSummary[];
+  appliedRemediation: string[];
+} {
   // Lowercase the upgrades object. This might be overly defensive, given that
   // we control this input internally, but its a low cost guard rail. Outputs a
   // mapping of upgrade to -> from, instead of the nested upgradeTo object.
@@ -20,8 +24,10 @@ export function generatePins(
     return {
       pinnedRequirements: [],
       changes: [],
+      appliedRemediation: [],
     };
   }
+  const appliedRemediation: string[] = [];
   const changes: FixChangesSummary[] = [];
   const pinnedRequirements = Object.keys(lowerCasedPins)
     .map((pkgNameAtVersion) => {
@@ -32,6 +38,7 @@ export function generatePins(
         success: true,
         userMessage: `Pinned ${pkgName} from ${version} to ${newVersion}`,
       });
+      appliedRemediation.push(pkgNameAtVersion);
       return `${newRequirement} # not directly required, pinned by Snyk to avoid a vulnerability`;
     })
     .filter(isDefined);
@@ -39,5 +46,6 @@ export function generatePins(
   return {
     pinnedRequirements,
     changes,
+    appliedRemediation,
   };
 }
diff --git a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-upgrades.ts b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-upgrades.ts
index fe37307dc7..62a5169bbc 100644
--- a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-upgrades.ts
+++ b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/generate-upgrades.ts
@@ -6,7 +6,12 @@ import { UpgradedRequirements } from './types';
 export function generateUpgrades(
   requirements: Requirement[],
   updates: DependencyPins,
-): { updatedRequirements: UpgradedRequirements; changes: FixChangesSummary[] } {
+  referenceFileInChanges?: string,
+): {
+  updatedRequirements: UpgradedRequirements;
+  changes: FixChangesSummary[];
+  appliedRemediation: string[];
+} {
   // Lowercase the upgrades object. This might be overly defensive, given that
   // we control this input internally, but its a low cost guard rail. Outputs a
   // mapping of upgrade to -> from, instead of the nested upgradeTo object.
@@ -19,9 +24,11 @@ export function generateUpgrades(
     return {
       updatedRequirements: {},
       changes: [],
+      appliedRemediation: [],
     };
   }
 
+  const appliedRemediation: string[] = [];
   const changes: FixChangesSummary[] = [];
   const updatedRequirements = {};
   requirements.map(
@@ -58,16 +65,22 @@ export function generateUpgrades(
       const updatedRequirement = `${originalName}${versionComparator}${newVersion}`;
       changes.push({
         success: true,
-        userMessage: `Upgraded ${originalName} from ${version} to ${newVersion}`,
+        userMessage: `Upgraded ${originalName} from ${version} to ${newVersion}${
+          referenceFileInChanges
+            ? ` (upgraded in ${referenceFileInChanges})`
+            : ''
+        }`,
       });
       updatedRequirements[originalText] = `${updatedRequirement}${
         extras ? extras : ''
       }`;
+      appliedRemediation.push(upgrade);
     },
   );
 
   return {
     updatedRequirements,
     changes,
+    appliedRemediation,
   };
 }
diff --git a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/index.ts b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/index.ts
index 383d90d6af..5b0fdda2c7 100644
--- a/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/index.ts
+++ b/packages/snyk-fix/src/plugins/python/handlers/pip-requirements/update-dependencies/index.ts
@@ -19,7 +19,13 @@ const debug = debugLib('snyk-fix:python:update-dependencies');
 export function updateDependencies(
   parsedRequirementsData: ParsedRequirements,
   updates: DependencyPins,
-): { updatedManifest: string; changes: FixChangesSummary[] } {
+  directUpgradesOnly = false,
+  referenceFileInChanges?: string,
+): {
+  updatedManifest: string;
+  changes: FixChangesSummary[];
+  appliedRemediation: string[];
+} {
   const {
     requirements,
     endsWithNewLine: shouldEndWithNewLine,
@@ -32,17 +38,24 @@ export function updateDependencies(
   }
   debug('Finished parsing manifest');
 
-  const { updatedRequirements, changes: upgradedChanges } = generateUpgrades(
-    requirements,
-    updates,
-  );
+  const {
+    updatedRequirements,
+    changes: upgradedChanges,
+    appliedRemediation,
+  } = generateUpgrades(requirements, updates, referenceFileInChanges);
   debug('Finished generating upgrades to apply');
 
-  const { pinnedRequirements, changes: pinChanges } = generatePins(
-    requirements,
-    updates,
-  );
-  debug('Finished generating pins to apply');
+  let pinnedRequirements: string[] = [];
+  let pinChanges: FixChangesSummary[] = [];
+  let appliedPinsRemediation: string[] = [];
+  if (!directUpgradesOnly) {
+    ({
+      pinnedRequirements,
+      changes: pinChanges,
+      appliedRemediation: appliedPinsRemediation,
+    } = generatePins(requirements, updates));
+    debug('Finished generating pins to apply');
+  }
 
   let updatedManifest = [
     ...applyUpgrades(requirements, updatedRequirements),
@@ -59,5 +72,6 @@ export function updateDependencies(
   return {
     updatedManifest,
     changes: [...pinChanges, ...upgradedChanges],
+    appliedRemediation: [...appliedPinsRemediation, ...appliedRemediation],
   };
 }
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/__snapshots__/update-dependencies.spec.ts.snap b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/__snapshots__/update-dependencies.spec.ts.snap
index 37ceccdf94..d554e57d51 100644
--- a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/__snapshots__/update-dependencies.spec.ts.snap
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/__snapshots__/update-dependencies.spec.ts.snap
@@ -1,5 +1,55 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`fix *req*.txt / *.txt Python projects fixes multiple files that are included via -r 1`] = `
+Array [
+  Object {
+    "success": true,
+    "userMessage": "Upgraded Django from 1.6.1 to 2.0.1",
+  },
+  Object {
+    "success": true,
+    "userMessage": "Upgraded Jinja2 from 2.7.2 to 2.7.3 (upgraded in base2.txt)",
+  },
+]
+`;
+
+exports[`fix *req*.txt / *.txt Python projects fixes multiple files via -r with the same name (some were already fixed) 1`] = `
+"Successful fixes:
+
+  app-with-already-fixed/requirements.txt
+  ✔ Upgraded Django from 1.6.1 to 2.0.1
+  ✔ Upgraded Django from 1.6.1 to 2.0.1 (upgraded in core/requirements.txt)
+  ✔ Upgraded Jinja2 from 2.7.2 to 2.7.3 (upgraded in lib/requirements.txt)
+
+  app-with-already-fixed/core/requirements.txt
+  ✔ Previously fixed
+
+  app-with-already-fixed/lib/requirements.txt
+  ✔ Previously fixed
+
+Summary:
+
+  0 items were not fixed
+  3 items were successfully fixed"
+`;
+
+exports[`fix *req*.txt / *.txt Python projects fixes multiple files via -r with the same name (some were already fixed) 2`] = `
+Array [
+  Object {
+    "success": true,
+    "userMessage": "Upgraded Django from 1.6.1 to 2.0.1",
+  },
+  Object {
+    "success": true,
+    "userMessage": "Upgraded Django from 1.6.1 to 2.0.1 (upgraded in core/requirements.txt)",
+  },
+  Object {
+    "success": true,
+    "userMessage": "Upgraded Jinja2 from 2.7.2 to 2.7.3 (upgraded in lib/requirements.txt)",
+  },
+]
+`;
+
 exports[`fix *req*.txt / *.txt Python projects retains python markers 1`] = `
 "amqp==2.4.2
 apscheduler==3.6.0
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/update-dependencies.spec.ts b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/update-dependencies.spec.ts
index 04fe080ad0..11fec6844e 100644
--- a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/update-dependencies.spec.ts
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/update-dependencies.spec.ts
@@ -1,6 +1,7 @@
 import * as fs from 'fs';
 import * as pathLib from 'path';
 import * as snykFix from '../../../../../src';
+import { TestResult } from '../../../../../src/types';
 import {
   generateScanResult,
   generateTestResult,
@@ -12,9 +13,13 @@ describe('fix *req*.txt / *.txt Python projects', () => {
     filesToDelete.map((f) => fs.unlinkSync(f));
   });
   const workspacesPath = pathLib.resolve(__dirname, 'workspaces');
-  it('skips projects with a -r option', async () => {
+
+  it('fixes project with a -r option', async () => {
     // Arrange
     const targetFile = 'with-require/dev.txt';
+    filesToDelete = [
+      pathLib.join(workspacesPath, 'with-require/fixed-dev.txt'),
+    ];
 
     const testResult = {
       ...generateTestResult(),
@@ -38,28 +43,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -72,15 +60,22 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       results: {
         python: {
           failed: [],
-          skipped: [
+          skipped: [],
+          succeeded: [
             {
               original: entityToFix,
-              userMessage: expect.stringContaining(
-                'directive are not yet supported',
-              ),
+              changes: [
+                {
+                  success: true,
+                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
+                },
+                {
+                  success: true,
+                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
+                },
+              ],
             },
           ],
-          succeeded: [],
         },
       },
     });
@@ -92,6 +87,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'basic/fixed-prod.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -115,28 +111,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -162,11 +141,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
               changes: [
                 {
                   success: true,
-                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
+                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
                 },
                 {
                   success: true,
-                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
+                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
                 },
               ],
             },
@@ -183,6 +162,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'basic-with-newline/fixed-prod.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -206,28 +186,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -253,11 +216,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
               changes: [
                 {
                   success: true,
-                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
+                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
                 },
                 {
                   success: true,
-                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
+                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
                 },
               ],
             },
@@ -274,6 +237,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'with-custom-formatting/fixed-requirements.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -297,28 +261,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -345,11 +292,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
               changes: [
                 {
                   success: true,
-                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
+                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
                 },
                 {
                   success: true,
-                  userMessage: 'Upgraded Django from 1.6.1 to 2.0.1',
+                  userMessage: 'Pinned transitive from 1.0.0 to 1.1.1',
                 },
               ],
             },
@@ -366,6 +313,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'lower-case-dep/fixed-req.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -384,28 +332,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -448,6 +379,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'basic/fixed-prod.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -467,28 +399,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -531,6 +446,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'long-versions/fixed-prod.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -549,28 +465,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -613,6 +512,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       workspacesPath,
       'with-comparator/fixed-prod.txt',
     );
+    filesToDelete = [fixedFilePath];
 
     const testResult = {
       ...generateTestResult(),
@@ -636,28 +536,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -704,6 +587,7 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       'python-markers/fixed-prod.txt',
     );
 
+    filesToDelete = [fixedFilePath];
     const testResult = {
       ...generateTestResult(),
       remediation: {
@@ -721,28 +605,11 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     };
 
-    const entityToFix = {
-      workspace: {
-        readFile: async (path: string) => {
-          return fs.readFileSync(
-            pathLib.resolve(workspacesPath, path),
-            'utf-8',
-          );
-        },
-        writeFile: async (path: string, contents: string) => {
-          const res = pathLib.parse(path);
-          const fixedPath = pathLib.resolve(
-            workspacesPath,
-            res.dir,
-            `fixed-${res.base}`,
-          );
-          filesToDelete = [fixedPath];
-          fs.writeFileSync(fixedPath, contents, 'utf-8');
-        },
-      },
-      scanResult: generateScanResult('pip', targetFile),
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
       testResult,
-    };
+    );
 
     // Act
     const result = await snykFix.fix([entityToFix], {
@@ -774,4 +641,166 @@ describe('fix *req*.txt / *.txt Python projects', () => {
       },
     });
   });
+  it('fixes multiple files that are included via -r', async () => {
+    // Arrange
+    const targetFile = 'pip-app/requirements.txt';
+    filesToDelete = [
+      pathLib.resolve(workspacesPath, 'pip-app/fixed-requirements.txt'),
+      pathLib.resolve(workspacesPath, 'pip-app/fixed-base2.txt'),
+    ];
+    const testResult = {
+      ...generateTestResult(),
+      remediation: {
+        unresolved: [],
+        upgrade: {},
+        patch: {},
+        ignore: {},
+        pin: {
+          'django@1.6.1': {
+            upgradeTo: 'django@2.0.1',
+            vulns: [],
+            isTransitive: false,
+          },
+          'Jinja2@2.7.2': {
+            upgradeTo: 'Jinja2@2.7.3',
+            vulns: [],
+            isTransitive: true,
+          },
+        },
+      },
+    };
+    const entityToFix = generateEntityToFix(
+      workspacesPath,
+      targetFile,
+      testResult,
+    );
+    const writeFileSpy = jest.spyOn(entityToFix.workspace, 'writeFile');
+
+    // Act
+    const result = await snykFix.fix([entityToFix], {
+      quiet: true,
+      stripAnsi: true,
+    });
+
+    // 2 files needed to have changes
+    expect(writeFileSpy).toHaveBeenCalledTimes(2);
+    expect(result.results.python.succeeded[0].original).toEqual(entityToFix);
+    expect(result.results.python.succeeded[0].changes).toMatchSnapshot();
+  });
+  it('fixes multiple files via -r with the same name (some were already fixed)', async () => {
+    // Arrange
+    const targetFile1 = 'app-with-already-fixed/requirements.txt';
+    const targetFile2 = 'app-with-already-fixed/lib/requirements.txt';
+    const targetFile3 = 'app-with-already-fixed/core/requirements.txt';
+
+    filesToDelete = [
+      pathLib.resolve(
+        workspacesPath,
+        'app-with-already-fixed/fixed-requirements.txt',
+      ),
+      pathLib.resolve(
+        workspacesPath,
+        'app-with-already-fixed/lib/fixed-requirements.txt',
+      ),
+      pathLib.resolve(
+        workspacesPath,
+        'app-with-already-fixed/core/fixed-requirements.txt',
+      ),
+    ];
+    const testResult = {
+      ...generateTestResult(),
+      remediation: {
+        unresolved: [],
+        upgrade: {},
+        patch: {},
+        ignore: {},
+        pin: {
+          'django@1.6.1': {
+            upgradeTo: 'django@2.0.1',
+            vulns: [],
+            isTransitive: false,
+          },
+          'Jinja2@2.7.2': {
+            upgradeTo: 'Jinja2@2.7.3',
+            vulns: [],
+            isTransitive: true,
+          },
+        },
+      },
+    };
+    const entityToFix1 = generateEntityToFix(
+      workspacesPath,
+      targetFile1,
+      testResult,
+    );
+    const entityToFix2 = generateEntityToFix(
+      workspacesPath,
+      targetFile2,
+      testResult,
+    );
+    const entityToFix3 = generateEntityToFix(
+      workspacesPath,
+      targetFile3,
+      testResult,
+    );
+    const writeFileSpy = jest.spyOn(entityToFix1.workspace, 'writeFile');
+    // Act
+    const result = await snykFix.fix(
+      [entityToFix2, entityToFix3, entityToFix1],
+      {
+        quiet: true,
+        stripAnsi: true,
+      },
+    );
+    // 3 files needed to have changes
+    expect(result.fixSummary).toMatchSnapshot();
+    expect(writeFileSpy).toHaveBeenCalledTimes(3);
+    expect(result.results.python.succeeded[0].original).toEqual(entityToFix1);
+    expect(result.results.python.succeeded[0].changes).toMatchSnapshot();
+  });
 });
+
+function readFileHelper(workspacesPath: string, path: string): string {
+  // because we write multiple time the file
+  // may be have already been updated in fixed-* name
+  // so try read that first
+  const res = pathLib.parse(path);
+  const fixedPath = pathLib.resolve(
+    workspacesPath,
+    res.dir,
+    `fixed-${res.base}`,
+  );
+  let file;
+  try {
+    file = fs.readFileSync(fixedPath, 'utf-8');
+  } catch (e) {
+    file = fs.readFileSync(pathLib.resolve(workspacesPath, path), 'utf-8');
+  }
+  return file;
+}
+
+function generateEntityToFix(
+  workspacesPath: string,
+  targetFile: string,
+  testResult: TestResult,
+): snykFix.EntityToFix {
+  const entityToFix = {
+    workspace: {
+      readFile: async (path: string) => {
+        return readFileHelper(workspacesPath, path);
+      },
+      writeFile: async (path: string, contents: string) => {
+        const res = pathLib.parse(path);
+        const fixedPath = pathLib.resolve(
+          workspacesPath,
+          res.dir,
+          `fixed-${res.base}`,
+        );
+        fs.writeFileSync(fixedPath, contents, 'utf-8');
+      },
+    },
+    scanResult: generateScanResult('pip', targetFile),
+    testResult,
+  };
+  return entityToFix;
+}
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/base.txt b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/base.txt
new file mode 100644
index 0000000000..aba69a5a27
--- /dev/null
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/base.txt
@@ -0,0 +1 @@
+click>7.0
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/core/requirements.txt b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/core/requirements.txt
new file mode 100644
index 0000000000..e5568357b9
--- /dev/null
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/core/requirements.txt
@@ -0,0 +1 @@
+Django==1.6.1 ; python_version > '1.0'
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/lib/requirements.txt b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/lib/requirements.txt
new file mode 100644
index 0000000000..c3eeef4fb7
--- /dev/null
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/lib/requirements.txt
@@ -0,0 +1 @@
+Jinja2==2.7.2
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/requirements.txt b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/requirements.txt
new file mode 100644
index 0000000000..3693dd3bd5
--- /dev/null
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/app-with-already-fixed/requirements.txt
@@ -0,0 +1,4 @@
+-r core/requirements.txt
+-r lib/requirements.txt
+-r base.txt
+Django==1.6.1
diff --git a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/pip-app/requirements.txt b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/pip-app/requirements.txt
index a8d089e1c8..44d5b49554 100644
--- a/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/pip-app/requirements.txt
+++ b/packages/snyk-fix/test/acceptance/plugins/python/update-dependencies/workspaces/pip-app/requirements.txt
@@ -1,2 +1,3 @@
 -r base.txt
+-r base2.txt
 Django==1.6.1
diff --git a/packages/snyk-fix/test/unit/fix.spec.ts b/packages/snyk-fix/test/unit/fix.spec.ts
index 6eb4df456b..b0d27fed6e 100644
--- a/packages/snyk-fix/test/unit/fix.spec.ts
+++ b/packages/snyk-fix/test/unit/fix.spec.ts
@@ -17,7 +17,7 @@ describe('Snyk fix', () => {
     });
 
     // Assert
-    expect(writeFileSpy).toHaveBeenCalled();
+    expect(writeFileSpy).toHaveBeenCalledTimes(1);
     expect(res.exceptions).toMatchSnapshot();
     expect(res.results).toMatchSnapshot();
   });
diff --git a/packages/snyk-fix/test/unit/plugins/python/handlers/update-dependencies/update-dependencies.spec.ts b/packages/snyk-fix/test/unit/plugins/python/handlers/update-dependencies/update-dependencies.spec.ts
index 2b65831213..133a9455d2 100644
--- a/packages/snyk-fix/test/unit/plugins/python/handlers/update-dependencies/update-dependencies.spec.ts
+++ b/packages/snyk-fix/test/unit/plugins/python/handlers/update-dependencies/update-dependencies.spec.ts
@@ -306,4 +306,40 @@ describe('remediation', () => {
       );
     }
   });
+  it('skips pins if asked', () => {
+    const upgrades = {
+      'django@1.6.1': {
+        upgradeTo: 'django@2.0.1',
+        vulns: [],
+        upgrades: [],
+        isTransitive: false,
+      },
+      'transitive@1.0.0': {
+        upgradeTo: 'transitive@1.1.1',
+        vulns: [],
+        upgrades: [],
+        isTransitive: true,
+      },
+    };
+
+    const manifestContents = 'Django==1.6.1';
+
+    const expectedManifest =
+      'Django==2.0.1\ntransitive>=1.1.1 # not directly required, pinned by Snyk to avoid a vulnerability';
+    const directUpgradesOnly = false;
+    const requirements = parseRequirementsFile(manifestContents);
+    const result = updateDependencies(
+      requirements,
+      upgrades,
+      directUpgradesOnly,
+    );
+    expect(result.changes.map((c) => c.userMessage).sort()).toEqual(
+      [
+        'Pinned transitive from 1.0.0 to 1.1.1',
+        'Upgraded Django from 1.6.1 to 2.0.1',
+      ].sort(),
+    );
+    // Note no extra newline was added to the expected manifest
+    expect(result.updatedManifest).toEqual(expectedManifest);
+  });
 });
diff --git a/packages/snyk-fix/test/unit/plugins/python/is-supported.ts b/packages/snyk-fix/test/unit/plugins/python/is-supported.spec.ts
similarity index 92%
rename from packages/snyk-fix/test/unit/plugins/python/is-supported.ts
rename to packages/snyk-fix/test/unit/plugins/python/is-supported.spec.ts
index fbb2210090..24cc508b40 100644
--- a/packages/snyk-fix/test/unit/plugins/python/is-supported.ts
+++ b/packages/snyk-fix/test/unit/plugins/python/is-supported.spec.ts
@@ -13,14 +13,14 @@ describe('isSupported', () => {
     const res = await isSupported(entity);
     expect(res.supported).toBeFalsy();
   });
-  it('with -r directive in the manifest not supported', async () => {
+  it('with -r directive in the manifest is supported', async () => {
     const entity = generateEntityToFix(
       'pip',
       'requirements.txt',
       '-r prod.txt\nDjango==1.6.1',
     );
     const res = await isSupported(entity);
-    expect(res.supported).toBeFalsy();
+    expect(res.supported).toBeTruthy();
   });
   it('with -c directive in the manifest not supported', async () => {
     const entity = generateEntityToFix(