diff --git a/src/Recording.ts b/src/Recording.ts
index cd835e3e..86e62855 100644
--- a/src/Recording.ts
+++ b/src/Recording.ts
@@ -6,7 +6,7 @@ import { inspect } from "node:util";
 import type AppMap from "./AppMap";
 import AppMapStream from "./AppMapStream";
 import { makeClassMap } from "./classMap";
-import { appMapDir } from "./config";
+import config from "./config";
 import { makeCallEvent, makeExceptionEvent, makeReturnEvent } from "./event";
 import { defaultMetadata } from "./metadata";
 import type { FunctionInfo } from "./registry";
@@ -16,7 +16,7 @@ export default class Recording {
   constructor(type: AppMap.RecorderType, recorder: string, ...names: string[]) {
     const dirs = [recorder, ...names].map(quotePathSegment);
     const name = dirs.pop()!; // it must have at least one element
-    this.path = join(appMapDir, ...dirs, makeAppMapFilename(name));
+    this.path = join(config.appmapDir, ...dirs, makeAppMapFilename(name));
     this.partPath = this.path + ".part";
     this.stream = new AppMapStream(this.partPath);
     this.metadata = {
diff --git a/src/bin.ts b/src/bin.ts
index 84761107..1fe4eda8 100644
--- a/src/bin.ts
+++ b/src/bin.ts
@@ -6,8 +6,9 @@ import { kill, pid } from "node:process";
 
 import { info } from "./message";
 import { version } from "./metadata";
-import { readPkgUp } from "./util/readPkgUp";
 import forwardSignals from "./util/forwardSignals";
+import { readPkgUp } from "./util/readPkgUp";
+import config from "./config";
 
 const registerPath = resolve(__dirname, "../dist/register.js");
 const loaderPath = resolve(__dirname, "../dist/loader.js");
@@ -19,6 +20,7 @@ export function main() {
 
   info("Running with appmap-node version %s", version);
   addNodeOptions("--require", registerPath);
+  config.export();
 
   // FIXME: Probably there should be a way to remove this altogether
   // by changing our custom loader implementation
diff --git a/src/config.ts b/src/config.ts
index 2d6156b0..90f30ee1 100644
--- a/src/config.ts
+++ b/src/config.ts
@@ -3,8 +3,19 @@ import { cwd } from "node:process";
 
 import { readPkgUp } from "./util/readPkgUp";
 
-export const root = cwd();
-export const appMapDir = join(root, "tmp", "appmap");
+export class Config {
+  public readonly appmapDir: string;
+  public readonly appName: string;
 
-export const targetPackage = readPkgUp(root);
-export const appName = targetPackage?.name ?? dirname(root);
+  constructor(public readonly root = process.env.APPMAP_ROOT ?? cwd()) {
+    this.appmapDir = join(root, "tmp", "appmap");
+    const targetPackage = readPkgUp(root);
+    this.appName = targetPackage?.name ?? dirname(root);
+  }
+
+  export() {
+    process.env.APPMAP_ROOT = this.root;
+  }
+}
+
+export default new Config();
diff --git a/src/hooks/__tests__/instrument.test.ts b/src/hooks/__tests__/instrument.test.ts
index 884348da..b7bf60b6 100644
--- a/src/hooks/__tests__/instrument.test.ts
+++ b/src/hooks/__tests__/instrument.test.ts
@@ -1,11 +1,12 @@
 import { full as walk } from "acorn-walk";
 import { ESTree, parse } from "meriyah";
 
-import * as instrument from "../instrument";
+import config from "../../config";
 import * as registry from "../../registry";
+import * as instrument from "../instrument";
 
 describe(instrument.shouldInstrument, () => {
-  instrument.setRoot("/test");
+  jest.replaceProperty(config, "root", "/test");
   test.each([
     ["node:test", false],
     ["file:///test/test.json", false],
@@ -125,3 +126,5 @@ function stripLocations(program: ESTree.Program): ESTree.Program {
   });
   return program;
 }
+
+jest.mock("../../config");
diff --git a/src/hooks/instrument.ts b/src/hooks/instrument.ts
index f134efbe..82522be4 100644
--- a/src/hooks/instrument.ts
+++ b/src/hooks/instrument.ts
@@ -1,12 +1,12 @@
 import assert from "node:assert";
 import path from "node:path";
-import { cwd } from "node:process";
 import { fileURLToPath } from "node:url";
 
 import { ancestor as walk } from "acorn-walk";
 import { ESTree, parse } from "meriyah";
 import { SourceMapConsumer } from "source-map-js";
 
+import config from "../config";
 import {
   args as args_,
   call_,
@@ -19,7 +19,7 @@ import {
   toArrowFunction,
   yieldStar,
 } from "../generate";
-import { FunctionInfo, SourceLocation, createMethodInfo, createFunctionInfo } from "../registry";
+import { FunctionInfo, SourceLocation, createFunctionInfo, createMethodInfo } from "../registry";
 import findLast from "../util/findLast";
 
 const __appmapFunctionRegistryIdentifier = identifier("__appmapFunctionRegistry");
@@ -147,19 +147,13 @@ function wrapWithRecord(
   return wrapped;
 }
 
-let root = cwd();
-
-export function setRoot(path: string) {
-  root = path;
-}
-
 export function shouldInstrument(url: URL): boolean {
   if (url.protocol !== "file:") return false;
   if (url.pathname.endsWith(".json")) return false;
 
   const filePath = fileURLToPath(url);
   if (filePath.includes("node_modules") || filePath.includes(".yarn")) return false;
-  if (isUnrelated(root, filePath)) return false;
+  if (isUnrelated(config.root, filePath)) return false;
 
   return true;
 }
diff --git a/src/loader.ts b/src/loader.ts
index f53b67ba..001b6a1a 100644
--- a/src/loader.ts
+++ b/src/loader.ts
@@ -1,11 +1,11 @@
-import path from "node:path";
-import { URL } from "node:url";
+import path, { dirname } from "node:path";
+import { URL, fileURLToPath } from "node:url";
 
 import type { NodeLoaderHooksAPI2 } from "ts-node";
 
-import { targetPackage } from "./config";
 import { warn } from "./message";
 import transform, { findHook } from "./transform";
+import { readPkgUp } from "./util/readPkgUp";
 
 export const load: NodeLoaderHooksAPI2["load"] = async function load(url, context, defaultLoad) {
   const urlObj = new URL(url);
@@ -15,9 +15,13 @@ export const load: NodeLoaderHooksAPI2["load"] = async function load(url, contex
   // CommonJS modules. This leads to TypeError [ERR_UNKNOWN_FILE_EXTENSION].
   // To fix this, we give the context.format hint to defaultLoad if we decide
   // that the file is a CommonJS module.
-  const ext = path.extname(urlObj.pathname).slice(1);
-  if (ext == "" && urlObj.protocol == "file:" && targetPackage?.type != "module") {
-    context.format = "commonjs";
+  if (urlObj.protocol === "file:") {
+    const targetPath = fileURLToPath(urlObj);
+    if (
+      path.extname(targetPath).slice(1) === "" &&
+      readPkgUp(dirname(targetPath))?.type !== "module"
+    )
+      context.format = "commonjs";
   }
 
   const hook = findHook(urlObj);
diff --git a/src/metadata.ts b/src/metadata.ts
index 4fa59b9c..4da74ee4 100644
--- a/src/metadata.ts
+++ b/src/metadata.ts
@@ -3,7 +3,7 @@ import process from "node:process";
 import type { PackageJson } from "type-fest";
 
 import type AppMap from "./AppMap";
-import { appName } from "./config";
+import config from "./config";
 import { examineException } from "./event";
 import pick from "./util/pick";
 
@@ -24,7 +24,7 @@ export const defaultMetadata: Partial<AppMap.Metadata> & { client: AppMap.Client
     engine: "Node.js",
     version: process.version,
   },
-  app: appName,
+  app: config.appName,
 };
 
 export function exceptionMetadata(error: unknown): AppMap.ExceptionMetadata | undefined {
diff --git a/test/simple.test.ts b/test/simple.test.ts
index 68390560..76a1f3dc 100644
--- a/test/simple.test.ts
+++ b/test/simple.test.ts
@@ -63,3 +63,10 @@ integrationTest("mapping an extensionless CommonJS file", () => {
   expect(runAppmapNode("./extensionless").status).toBe(0);
   expect(readAppmap()).toMatchSnapshot();
 });
+
+integrationTest("running a script after changing the current directory", () => {
+  // Need to make sure the appmap "root" stays the same after
+  // appmap-node is run, even if the current directory changes.
+  expect(runAppmapNode("bash", "-c", "cd subproject; node index.js").status).toBe(0);
+  expect(readAppmap()).toBeDefined();
+});
diff --git a/test/simple/subproject/index.js b/test/simple/subproject/index.js
new file mode 120000
index 00000000..e234193f
--- /dev/null
+++ b/test/simple/subproject/index.js
@@ -0,0 +1 @@
+../index.js
\ No newline at end of file