diff --git a/.github/scripts/check-pr-linked-issue.mjs b/.github/scripts/check-pr-linked-issue.mjs
new file mode 100644
index 00000000..865b8865
--- /dev/null
+++ b/.github/scripts/check-pr-linked-issue.mjs
@@ -0,0 +1,53 @@
+#!/usr/bin/env node
+/**
+ * check-pr-linked-issue.mjs
+ * Checks that a PR body references a GitHub issue. Respects conventional commit
+ * prefixes — skips check for docs/chore/build/ci/style/test prefixed PRs.
+ * Export: checkLinkedIssue(prBody: string, prTitle: string) → { passed, failures }
+ */
+import { fileURLToPath } from 'node:url';
+
+const ISSUE_PATTERNS = [
+  /(?:fixes|closes|resolves)\s+#\d+/i,
+  /(?:^|[\s(])https:\/\/github\.com\/paperclipai\/paperclip\/issues\/\d+(?=$|[\s),:;!?]|[.](?![\w-]))/i,
+  /(?<!\w)#\d+/,
+];
+
+// Prefixes where a linked issue is NOT required
+const SKIP_ISSUE_PREFIXES = ['docs', 'chore', 'build', 'ci', 'style', 'test', 'revert'];
+
+function parsePrefix(title) {
+  if (!title) return null;
+  const match = title.match(/^([a-z]+)(?:\([^)]*\))?:/);
+  return match ? match[1].toLowerCase() : null;
+}
+
+export function checkLinkedIssue(body, prTitle = '') {
+  const prefix = parsePrefix(prTitle);
+
+  if (prefix && SKIP_ISSUE_PREFIXES.includes(prefix)) {
+    return { passed: true, failures: [] };
+  }
+
+  if (!body || !body.trim()) {
+    return { passed: false, failures: ['PR body is empty — please fill out the PR template'] };
+  }
+
+  const found = ISSUE_PATTERNS.some(p => p.test(body));
+  return {
+    passed: found,
+    failures: found ? [] : [
+      'No linked issue found — please add `Fixes #NNN` to your PR description. ' +
+      'If no issue exists yet, please file one first: ' +
+      'https://github.com/paperclipai/paperclip/issues/new',
+    ],
+  };
+}
+
+if (process.argv[1] === fileURLToPath(import.meta.url)) {
+  const body = process.env.PR_BODY ?? '';
+  const title = process.env.PR_TITLE ?? '';
+  const result = checkLinkedIssue(body, title);
+  console.log(JSON.stringify(result));
+  process.exit(result.passed ? 0 : 1);
+}
diff --git a/.github/scripts/run-quality-gates.mjs b/.github/scripts/run-quality-gates.mjs
index 8cf1ad09..a5b6abae 100644
--- a/.github/scripts/run-quality-gates.mjs
+++ b/.github/scripts/run-quality-gates.mjs
@@ -11,6 +11,7 @@ import { fileURLToPath } from 'node:url';
 import { ghFetch } from './get-bot-token.mjs';
 import { fetchAllPullRequestFiles } from './fetch-pr-files.mjs';
 import { checkTemplate } from './check-pr-template.mjs';
+import { checkLinkedIssue } from './check-pr-linked-issue.mjs';
 import { checkTestCoverage } from './check-pr-test-coverage.mjs';
 import { checkLockfile } from './check-pr-lockfile.mjs';
 import { checkDependencies } from './check-pr-dependencies.mjs';
@@ -109,9 +110,10 @@ async function main() {
 
   // Run all quality gates (pure functions run sync, deps check is async)
   const prTitle = pr.title ?? '';
-  const [templateResult, testResult, lockfileResult, depsResult] =
+  const [templateResult, issueResult, testResult, lockfileResult, depsResult] =
     await Promise.all([
       Promise.resolve(checkTemplate(prBody)),
+      Promise.resolve(checkLinkedIssue(prBody, prTitle)),
       Promise.resolve(checkTestCoverage(files, prTitle)),
       Promise.resolve(checkLockfile(files, author, branch)),
       checkDependencies(files, GH_TOKEN, GH_REPO, prNumber, pr.base?.ref),
@@ -119,6 +121,7 @@ async function main() {
 
   const allFailures = [
     ...templateResult.failures,
+    ...issueResult.failures,
     ...testResult.failures,
     ...lockfileResult.failures,
   ];
diff --git a/.github/scripts/tests/check-pr-linked-issue.test.mjs b/.github/scripts/tests/check-pr-linked-issue.test.mjs
new file mode 100644
index 00000000..6b2745db
--- /dev/null
+++ b/.github/scripts/tests/check-pr-linked-issue.test.mjs
@@ -0,0 +1,111 @@
+import { test } from 'node:test';
+import assert from 'node:assert/strict';
+import { checkLinkedIssue } from '../check-pr-linked-issue.mjs';
+
+// Existing tests with title parameter added (defaults to no prefix, so still required)
+
+test('passes with bare #NNN reference', () => {
+  assert.equal(checkLinkedIssue('This fixes the bug in #123', 'fix: something').passed, true);
+});
+
+test('passes with "Fixes #NNN"', () => {
+  assert.equal(checkLinkedIssue('Fixes #456\n\nSome description', 'fix: something').passed, true);
+});
+
+test('passes with "Closes #NNN" (case-insensitive)', () => {
+  assert.equal(checkLinkedIssue('closes #789', 'fix: something').passed, true);
+});
+
+test('passes with "Resolves #NNN"', () => {
+  assert.equal(checkLinkedIssue('Resolves #101', 'fix: something').passed, true);
+});
+
+test('passes with full github.com URL', () => {
+  assert.equal(
+    checkLinkedIssue('See https://github.com/paperclipai/paperclip/issues/202', 'fix: bug').passed,
+    true
+  );
+});
+
+test('passes with a full github.com URL followed by punctuation', () => {
+  assert.equal(
+    checkLinkedIssue('See (https://github.com/paperclipai/paperclip/issues/202).', 'fix: bug').passed,
+    true
+  );
+});
+
+test('fails with empty body when no skip prefix', () => {
+  const result = checkLinkedIssue('', 'fix: bug');
+  assert.equal(result.passed, false);
+  assert.ok(result.failures.length > 0);
+});
+
+test('fails with no issue reference when no skip prefix', () => {
+  const result = checkLinkedIssue('Added a cool feature, no issue linked', 'feat: something');
+  assert.equal(result.passed, false);
+  assert.ok(result.failures[0].includes('Fixes #NNN'));
+});
+
+test('fails with cross-repo issue reference', () => {
+  const result = checkLinkedIssue('See https://github.com/other/repo/issues/123', 'fix: bug');
+  assert.equal(result.passed, false);
+});
+
+test('fails when the Paperclip issue URL is embedded inside another host', () => {
+  const result = checkLinkedIssue(
+    'See https://evil.example/https://github.com/paperclipai/paperclip/issues/123',
+    'fix: bug'
+  );
+  assert.equal(result.passed, false);
+});
+
+test('fails when the Paperclip issue URL continues into another host', () => {
+  const result = checkLinkedIssue(
+    'See https://github.com/paperclipai/paperclip/issues/123.evil.example',
+    'fix: bug'
+  );
+  assert.equal(result.passed, false);
+});
+
+test('fails when #NNN is part of a word (no space before)', () => {
+  const result = checkLinkedIssue('This is version#123 not an issue link', 'fix: bug');
+  assert.equal(result.passed, false);
+});
+
+// New tests for prefix-aware skip behavior
+
+test('skips check for docs: prefix', () => {
+  assert.equal(checkLinkedIssue('', 'docs: update README').passed, true);
+});
+
+test('skips check for chore: prefix', () => {
+  assert.equal(checkLinkedIssue('', 'chore: bump deps').passed, true);
+});
+
+test('skips check for build: prefix', () => {
+  assert.equal(checkLinkedIssue('', 'build: update Dockerfile').passed, true);
+});
+
+test('skips check for ci: prefix', () => {
+  assert.equal(checkLinkedIssue('', 'ci: add workflow').passed, true);
+});
+
+test('skips check for test: prefix', () => {
+  assert.equal(checkLinkedIssue('', 'test: add coverage').passed, true);
+});
+
+test('skips check with scoped prefix like docs(api):', () => {
+  assert.equal(checkLinkedIssue('', 'docs(api): document endpoint').passed, true);
+});
+
+test('requires issue for feat: prefix', () => {
+  assert.equal(checkLinkedIssue('Some description without issue', 'feat: new thing').passed, false);
+});
+
+test('requires issue for refactor: prefix', () => {
+  assert.equal(checkLinkedIssue('Some refactor', 'refactor: rewrite thing').passed, false);
+});
+
+test('requires issue when no prefix (encourages prefix usage)', () => {
+  assert.equal(checkLinkedIssue('No prefix here', 'Add some feature').passed, false);
+});