diff --git a/assets/settings.yml b/assets/settings.yml
deleted file mode 100644
index f63d723..0000000
--- a/assets/settings.yml
+++ /dev/null
@@ -1,87 +0,0 @@
----
-# https://github.com/github/safe-settings/blob/main-enterprise/docs/sample-settings/settings.yml
-repository:
-  allow_squash_merge: false
-  allow_merge_commit: true
-  allow_rebase_merge: false
-  allow_auto_merge: true
-  delete_branch_on_merge: true
-
-# rulesets can have exceptions for flowzone-app to bypass policies
-# https://github.com/github/safe-settings/blob/main-enterprise/docs/sample-settings/org-ruleset.yml
-rulesets:
-  - name: "policy-bot: main"
-    target: branch
-    enforcement: active
-    conditions:
-      ref_name:
-        include:
-          - refs/heads/main
-        exclude: []
-      repository_name:
-        include:
-          - ~ALL
-        exclude: []
-    rules:
-      - type: required_status_checks
-        parameters:
-          strict_required_status_checks_policy: true
-          required_status_checks:
-            - context: "policy-bot: main"
-              integration_id: 278558
-            - context: "Flowzone / All jobs"
-      - type: pull_request
-        parameters:
-          required_approving_review_count: 0
-          dismiss_stale_reviews_on_push: false
-          require_code_owner_review: false
-          require_last_push_approval: false
-          required_review_thread_resolution: false
-    bypass_actors:
-      - actor_id: 1
-        actor_type: OrganizationAdmin
-        bypass_mode: always
-      - actor_id: 5
-        actor_type: RepositoryRole
-        bypass_mode: always
-      - actor_id: 291899
-        actor_type: Integration
-        bypass_mode: always
-
-  - name: "policy-bot: master"
-    target: branch
-    enforcement: active
-    conditions:
-      ref_name:
-        include:
-          - refs/heads/master
-        exclude: []
-      repository_name:
-        include:
-          - ~ALL
-        exclude: []
-    rules:
-      - type: required_status_checks
-        parameters:
-          strict_required_status_checks_policy: true
-          required_status_checks:
-            - context: "policy-bot: master"
-              integration_id: 278558
-            - context: "Flowzone / All jobs"
-      - type: pull_request
-        parameters:
-          required_approving_review_count: 0
-          dismiss_stale_reviews_on_push: false
-          require_code_owner_review: false
-          require_last_push_approval: false
-          required_review_thread_resolution: false
-    bypass_actors:
-      - actor_id: 1
-        actor_type: OrganizationAdmin
-        bypass_mode: always
-      - actor_id: 5
-        actor_type: RepositoryRole
-        bypass_mode: always
-      - actor_id: 291899
-        actor_type: Integration
-        bypass_mode: always
diff --git a/index.mjs b/index.mjs
index 4c924ac..8d5df66 100644
--- a/index.mjs
+++ b/index.mjs
@@ -12,205 +12,161 @@ const org = process.env.ORG_NAME;
 const specificRepo = process.env.SPECIFIC_REPO; // Optionally set this to run on a single repo
 const reposDir = path.join(process.cwd(), ".github", "repos");
 
-// https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-rulesets/creating-rulesets-for-a-repository#using-fnmatch-syntax
-const protectedBranches = [
-  {
-    name: "Default",
-    source: "~DEFAULT_BRANCH",
-    include: "~DEFAULT_BRANCH",
-  },
-  {
-    name: "ESR",
-    source: "2024.7.x",
-    include: "refs/heads/20[0-9][0-9].*.x",
-  }
-];
-
 // Initialize Octokit with the GitHub token
 const octokit = new Octokit({ auth: token });
 
-async function processRepository(repoName) {
-  let rulesets = [];
-  let branches = [];
-
-  // Fetch repository settings
-  const repoData = await octokit.rest.repos.get({ owner: org, repo: repoName });
-
-  if (repoData.data.archived) {
-    // Skip archived repositories
-    return;
-  }
+function branchRuleToNewBranch(query) {
+  const branchData = {
+    name: query.pattern,
+    protection: {
+      enforce_admins: query.isAdminEnforced,
+      required_pull_request_reviews: null,
+      restrictions: null,
+      required_status_checks: {
+        strict: true,
+        checks: [],
+      },
+    },
+  };
 
-  if ([".github"].includes(repoData.data.name)) {
-    // Skip the .github repository
-    return;
+  if (query.requiresStatusChecks) {
+    branchData.protection.required_status_checks.strict =
+      query.requiresStrictStatusChecks;
+    branchData.protection.required_status_checks.checks =
+      query.requiredStatusCheckContexts;
   }
 
-  console.log(`Processing repository: ${repoName}`);
-
-  for (const branch of protectedBranches) {
+  return branchData;
+}
 
-    let protectionData = {
-      data: {
-        required_status_checks: {
-          checks: [],
-          strict: true,
-        },
-      }
-    };
-
-    // Attempt to fetch branch protection data for the provided
-    // branch name. If the branch protection data is not found,
-    // attempt to fetch the branch protection data for the default
-    // branch of the repository.
-    try {
-      protectionData = await octokit.rest.repos.getBranchProtection({
-        owner: org,
-        repo: repoName,
-        branch: branch.source,
-      });
-    } catch (error) {
-      try {
-        protectionData = await octokit.rest.repos.getBranchProtection({
-          owner: org,
-          repo: repoName,
-          branch: repoData.data.default_branch,
-        });
-      } catch (error) {
-        // ignore errors
+async function getBranchProtectionRulesData(owner, repo) {
+  const query = `
+    query($owner: String!, $repo: String!) {
+      repository(owner: $owner, name: $repo) {
+        branchProtectionRules(first: 100) {
+          nodes {
+            pattern
+            requiresApprovingReviews
+            requiredApprovingReviewCount
+            requiresStatusChecks
+            requiredStatusCheckContexts
+            requiresStrictStatusChecks
+            restrictsPushes
+            restrictsReviewDismissals
+            isAdminEnforced
+          }
+        }
       }
     }
+  `;
 
-    const rulesetData = protectionDataToRuleset(protectionData.data, branch);
-
-    // Remove 'policy-bot' contexts and filter out rules without contexts
-    rulesetData.rules = rulesetData.rules
-      .map((rule) => {
-        if (rule.type === "required_status_checks") {
-          rule.parameters.required_status_checks =
-            rule.parameters.required_status_checks.filter(
-              (check) =>
-                !check.context.startsWith("policy-bot") &&
-                !check.context.startsWith("VersionBot") &&
-                !check.context.startsWith("ResinCI") &&
-                !check.context.startsWith("Flowzone")
-            );
-        }
-        return rule;
-      })
-      .filter(
-        (rule) =>
-          !(
-            rule.type === "required_status_checks" &&
-            rule.parameters.required_status_checks.length === 0
-          )
-      );
-
-    // Only push to rulesets if there are rules remaining after filters
-    if (rulesetData.rules.length > 0) {
-      rulesets.push(rulesetData);
-    }
+  try {
+    const result = await octokit.graphql(query, {
+      owner: owner,
+      repo: repo,
+    });
+
+    return result.repository.branchProtectionRules.nodes;
+  } catch (error) {
+    console.error(error);
   }
+}
 
+async function getRepoRulesetsData(owner, repo) {
   try {
-    const repoRulesets = await octokit.rest.repos.getRepoRulesets({
-      owner: org,
-      repo: repoName,
-      includes_parents: true,
+    const result = await octokit.rest.repos.getRepoRulesets({
+      owner: owner,
+      repo: repo,
+      includes_parents: false,
     });
 
-    repoRulesets.data = repoRulesets.data.filter(
-      (ruleset) => !ruleset.name.startsWith("policy-bot:")
-    );
-
-    for (let i = 0; i < repoRulesets.data.length; ++i) {
-      const rulesetResponse = await octokit.rest.repos.getRepoRuleset({
-        owner: org,
-        repo: repoName,
-        ruleset_id: repoRulesets.data[i].id,
-      });
-
-      delete rulesetResponse.data.id;
-      delete rulesetResponse.data.source;
-      delete rulesetResponse.data.source_type;
-      delete rulesetResponse.data.created_at;
-      delete rulesetResponse.data.updated_at;
-      delete rulesetResponse.data.node_id;
-      delete rulesetResponse.data.current_user_can_bypass;
-      delete rulesetResponse.data._links;
-
-      // Filter out context checks starting with Flowzone
-      rulesetResponse.data.rules = rulesetResponse.data.rules
-      .map((rule) => {
-        if (rule.type === "required_status_checks") {
-          rule.parameters.required_status_checks =
-            rule.parameters.required_status_checks.filter(
-              (check) =>
-                !check.context.startsWith("policy-bot") &&
-                !check.context.startsWith("VersionBot") &&
-                !check.context.startsWith("ResinCI") &&
-                !check.context.startsWith("Flowzone")
-            );
-        }
-        return rule;
-      })
-      .filter(
-        (rule) =>
-          !(
-            rule.type === "required_status_checks" &&
-            rule.parameters.required_status_checks.length === 0
-          )
-      );
-
-      if (rulesetResponse.data.rules.length < 1) {
-        // Skip rulesets without rules
-        continue;
-      }
+    return result.data;
+  } catch (error) {
+    console.error(error);
+  }
+}
 
-      // Skip rulesets without required_status_checks
-      if (
-        !rulesetResponse.data.rules.some(
-          (rule) => rule.type === "required_status_checks"
-        )
-      ) {
-        continue;
-      }
+async function getRulesetData(owner, repo, rulesetId) {
+  try {
+    const result = await octokit.rest.repos.getRepoRuleset({
+      owner: owner,
+      repo: repo,
+      ruleset_id: rulesetId,
+    });
 
-      if (rulesetResponse.data.name === "Default" && rulesetResponse.data.enforcement === "active") {
-        // Remove branch protection for the default branch if an active ruleset exists
-        branches.push({name: "default", protection: null});
-      };
+    return result.data;
+  } catch (error) {
+    console.error(error);
+  }
+}
 
-      if (rulesetResponse.data.name === "ESR" && rulesetResponse.data.enforcement === "active") {
-        // Remove branch protection for the ESR branch if an active ruleset exists
-        branches.push({name: "20*.*", protection: null});
-      };
+function rulesetDataToNewRuleset(rulesetData) {
+  delete rulesetData.id;
+  delete rulesetData.source;
+  delete rulesetData.source_type;
+  delete rulesetData.created_at;
+  delete rulesetData.updated_at;
+  delete rulesetData.node_id;
+  delete rulesetData.current_user_can_bypass;
+  delete rulesetData._links;
+  return rulesetData;
+}
 
-      // Skip existing rulesets with the name "ESR" or "Default" as we are reapplying them
-      // and duplicates are not allowed
-      if (["ESR","Default"].includes(rulesetResponse.data.name)) {
-        continue;
-      }
+async function getRepoData(owner, repo) {
+  try {
+    const result = await octokit.rest.repos.get({
+      owner: owner,
+      repo: repo,
+    });
 
-      rulesets.push(rulesetResponse.data);
-    }
+    return result.data;
   } catch (error) {
-    // ignore errors
     console.error(error);
   }
+}
+
+async function processRepository(repoName) {
+  let rulesets = [];
+  let branches = [];
 
-  if (rulesets.length < 1) {
-    // Skip repositories without rulesets
+  // Fetch repository settings
+  const repoData = await getRepoData(org, repoName);
+
+  if (repoData.archived) {
+    // Skip archived repositories
     return;
   }
 
+  if ([".github"].includes(repoData.name)) {
+    // Skip the .github repository
+    return;
+  }
+
+  console.log(`Processing repository: ${repoName}`);
+
+  const branchRulesData = await getBranchProtectionRulesData(org, repoName);
+  for (const branchRule of branchRulesData) {
+    const newBranch = branchRuleToNewBranch(branchRule);
+    branches.push(newBranch);
+  }
+
+  const repoRulesetsData = await getRepoRulesetsData(org, repoName);
+  for (const ruleset of repoRulesetsData) {
+    const rulesetData = await getRulesetData(org, repoName, ruleset.id);
+    const newRuleset = rulesetDataToNewRuleset(rulesetData);
+    rulesets.push(newRuleset);
+  }
+
   const jsonData = {};
-  jsonData.rulesets = rulesets;
 
   if (branches.length > 0) {
     jsonData.branches = branches;
   }
 
+  if (rulesets.length > 0) {
+    jsonData.rulesets = rulesets;
+  }
+
   const filePath = path.join(reposDir, `${repoName}.yml`);
 
   // Retain any existing props from the repo settings file that are not rulesets or branches
@@ -223,11 +179,20 @@ async function processRepository(repoName) {
     }
   }
 
+  function isEmptyObject(obj) {
+    return Object.keys(obj).length === 0 && obj.constructor === Object;
+  }
+
+  // return if jsonData is an empty object
+  if (isEmptyObject(jsonData)) {
+    return;
+  }
+
   const yamlData = yaml.stringify(jsonData);
   fs.writeFileSync(filePath, yamlData, "utf8");
 }
 
-async function fetchRepoSettings() {
+async function main() {
   if (!fs.existsSync(reposDir)) {
     fs.mkdirSync(reposDir);
   }
@@ -253,82 +218,4 @@ async function fetchRepoSettings() {
   console.log("Repository settings processing complete.");
 }
 
-async function main() {
-  // replace the file at orgSettingsPath with the one bundled with this npm package
-  // const yamlData = fs.readFileSync(packageSettingsPath, "utf8");
-  // fs.writeFileSync(orgSettingsPath, yamlData, "utf8");
-  await fetchRepoSettings();
-}
-
 main();
-
-function protectionDataToRuleset(protectionData, branch) {
-  const ruleset = {
-    name: branch.name,
-    target: "branch",
-    enforcement: "active",
-    conditions: {
-      ref_name: {
-        exclude: [],
-        include: [branch.include],
-      },
-    },
-    rules: [],
-    bypass_actors: [
-      {
-        actor_id: 1,
-        actor_type: "OrganizationAdmin",
-        bypass_mode: "always",
-      },
-      {
-        actor_id: 5,
-        actor_type: "RepositoryRole",
-        bypass_mode: "always",
-      },
-      {
-        actor_id: 291899,
-        actor_type: "Integration",
-        bypass_mode: "always",
-      },
-    ],
-  };
-
-  // Rule for required status checks
-  if (protectionData.required_status_checks) {
-    const statusChecksRule = {
-      type: "required_status_checks",
-      parameters: {
-        // strict_required_status_checks_policy:
-        //   protectionData.required_status_checks.strict,
-        strict_required_status_checks_policy: true,
-        required_status_checks:
-          protectionData.required_status_checks.checks.map((check) => ({
-            context: check.context,
-          })),
-      },
-    };
-    ruleset.rules.push(statusChecksRule);
-  }
-
-  // // Rule for pull request reviews
-  // if (protectionData.required_pull_request_reviews) {
-  //   const prReviewsRule = {
-  //     type: "pull_request",
-  //     parameters: {
-  //       required_approving_review_count: 0,
-  //       dismiss_stale_reviews_on_push:
-  //         protectionData.required_pull_request_reviews.dismiss_stale_reviews,
-  //       require_code_owner_review:
-  //         protectionData.required_pull_request_reviews
-  //           .require_code_owner_reviews,
-  //       require_last_push_approval:
-  //         protectionData.required_pull_request_reviews
-  //           .require_last_push_approval,
-  //       required_review_thread_resolution: false, // Set as needed
-  //     },
-  //   };
-  //   ruleset.rules.push(prReviewsRule);
-  // }
-
-  return ruleset;
-}
diff --git a/package-lock.json b/package-lock.json
index cd66fca..ee09499 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -9,6 +9,7 @@
       "version": "0.0.31",
       "license": "Apache-2.0",
       "dependencies": {
+        "@octokit/plugin-throttling": "^9.3.1",
         "dotenv": "^16.3.1",
         "octokit": "^4.0.2",
         "rimraf": "^6.0.0",
diff --git a/package.json b/package.json
index 36737c5..28d4351 100644
--- a/package.json
+++ b/package.json
@@ -6,9 +6,6 @@
   "main": "index.mjs",
   "bin": "index.mjs",
   "type": "module",
-  "files": [
-    "assets/settings.yml"
-  ],
   "scripts": {
     "test": "echo \"Error: no test specified\" && exit 0",
     "start": "npm run clean && node index.mjs",
@@ -29,6 +26,7 @@
   },
   "homepage": "https://github.com/product-os/safe-settings-bootstrap#readme",
   "dependencies": {
+    "@octokit/plugin-throttling": "^9.3.1",
     "dotenv": "^16.3.1",
     "octokit": "^4.0.2",
     "rimraf": "^6.0.0",