diff --git a/packages/gittensory-engine/src/signals/predicted-gate-engine.ts b/packages/gittensory-engine/src/signals/predicted-gate-engine.ts
index fc086bcafd..68df362c06 100644
--- a/packages/gittensory-engine/src/signals/predicted-gate-engine.ts
+++ b/packages/gittensory-engine/src/signals/predicted-gate-engine.ts
@@ -899,15 +899,21 @@ export function tokenize(value: string): string[] {
 }
 
 function extractLinkedIssueNumbers(text: string, repoFullName: string): number[] {
-  const numbers = [...text.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+#(\d+)\b/gi)].map((match) => Number(match[1]));
-  // GitHub also auto-closes via the fully-qualified `KEYWORD owner/repo#N` form (e.g. Renovate/Dependabot bodies).
-  // Count it only when owner/repo case-insensitively equals THIS repo — a reference to a different repo closes an
-  // issue elsewhere, not here, so it must not spoof a same-repo link. Same `\b`-anchored keywords as above (#1988).
+  // Strip inline code spans before scanning — mirrors src/db/repositories.ts (#4039) so the PR template's
+  // literal `(e.g. \`Closes #123\`)` checklist example does not spuriously link issue #123.
+  const withoutCodeSpans = text.replace(/`[^`\n]*`/g, " ");
   const target = repoFullName.toLowerCase();
-  for (const match of text.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+([\w.-]+\/[\w.-]+)#(\d+)\b/gi)) {
-    if (match[1]!.toLowerCase() === target) numbers.push(Number(match[2]));
+  const linkedIssues: number[] = [];
+  const seen = new Set<number>();
+  for (const match of withoutCodeSpans.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+(?:([\w.-]+\/[\w.-]+)#|#)(\d+)\b/gi)) {
+    const owner = match[1];
+    if (owner && owner.toLowerCase() !== target) continue;
+    const value = Number(match[2]);
+    if (!Number.isInteger(value) || value <= 0 || seen.has(value)) continue;
+    seen.add(value);
+    linkedIssues.push(value);
   }
-  return [...new Set(numbers.filter((value) => Number.isInteger(value) && value > 0))];
+  return linkedIssues;
 }
 
 function isMaintainerAssociation(value: string | null | undefined): boolean {
diff --git a/packages/gittensory-mcp/lib/local-branch.js b/packages/gittensory-mcp/lib/local-branch.js
index 492e8b4dcf..4421c33401 100644
--- a/packages/gittensory-mcp/lib/local-branch.js
+++ b/packages/gittensory-mcp/lib/local-branch.js
@@ -56,7 +56,7 @@ export function collectLocalBranchMetadata(input) {
   const ciStatusHints = input.ciStatusHints ?? collectCiStatusHints(cwd, baseRef, changedFiles);
   const commitMessages = input.commitMessages ?? collectCommitMessages(cwd, baseRef);
   const title = input.title ?? titleFromBranch(branchName) ?? firstCommitTitle(commitMessages);
-  const linkedIssues = [...new Set([...(input.linkedIssues ?? []), ...extractLinkedIssues([branchName, title, input.body, ...commitMessages].filter(Boolean).join("\n"))])].sort(
+  const linkedIssues = [...new Set([...(input.linkedIssues ?? []), ...extractLinkedIssues([branchName, title, input.body, ...commitMessages].filter(Boolean).join("\n"), repoFullName)])].sort(
     (left, right) => left - right,
   );
   const payload = {
@@ -557,14 +557,23 @@ function assertSourceUploadDisabled() {
   }
 }
 
-// Word-boundary the closing keywords (as the server-side extractors in src/db/repositories.ts and
-// src/signals/engine.ts already do) so a keyword embedded in a longer word does not spuriously link an
-// issue: without \b, `hotfix 5` / `prefixes 12` matched the `fix`/`fixes` substring and captured the
-// trailing number. The bare `#` branch stays boundary-free so `#123` still matches anywhere.
-export function extractLinkedIssues(text) {
-  const issues = [];
-  for (const match of String(text).matchAll(/(?:\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)|#)\s*#?(\d+)/gi)) issues.push(Number(match[1]));
-  return issues.filter((issue) => Number.isInteger(issue) && issue > 0);
+// Mirror src/db/repositories.ts extractLinkedIssueNumbersWithOverflow: strip inline code spans before
+// scanning (PR template checklist contains `(e.g. \`Closes #123\`)`), honor qualified owner/repo#N only
+// when it matches THIS repo, and word-boundary closing keywords so `hotfix 5` does not spoof a link.
+export function extractLinkedIssues(text, repoFullName = "") {
+  const target = String(repoFullName).toLowerCase();
+  const withoutCodeSpans = String(text).replace(/`[^`\n]*`/g, " ");
+  const linkedIssues = [];
+  const seen = new Set();
+  for (const match of withoutCodeSpans.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+(?:([\w.-]+\/[\w.-]+)#|#)(\d+)\b/gi)) {
+    const owner = match[1];
+    if (owner && owner.toLowerCase() !== target) continue;
+    const value = Number(match[2]);
+    if (!Number.isInteger(value) || value <= 0 || seen.has(value)) continue;
+    seen.add(value);
+    linkedIssues.push(value);
+  }
+  return linkedIssues;
 }
 
 function statusFromCode(code) {
diff --git a/test/unit/local-branch.test.ts b/test/unit/local-branch.test.ts
index dc93def9b8..22524ece13 100644
--- a/test/unit/local-branch.test.ts
+++ b/test/unit/local-branch.test.ts
@@ -1797,16 +1797,27 @@ describe("local MCP git metadata collection", () => {
   it("extracts linked issues only from standalone closing keywords, not keyword substrings", async () => {
     // @ts-expect-error package helper is plain JS because the local wrapper ships as a Node bin package.
     const { extractLinkedIssues } = await import("../../packages/gittensory-mcp/lib/local-branch.js");
-    // Standalone closing keywords (hash optional, as this client-side extractor allows) and bare #refs link.
-    expect(extractLinkedIssues("fixes #5")).toEqual([5]);
-    expect(extractLinkedIssues("Closes 12 and resolves #34")).toEqual([12, 34]);
-    expect(extractLinkedIssues("see #7")).toEqual([7]);
-    expect(extractLinkedIssues("closes#3")).toEqual([3]);
+    const repo = "owner/repo";
+    // Standalone closing keywords (hash optional) link when scoped to this repo.
+    expect(extractLinkedIssues("fixes #5", repo)).toEqual([5]);
+    expect(extractLinkedIssues("Closes #12 and resolves #34", repo)).toEqual([12, 34]);
+    expect(extractLinkedIssues("closes #3", repo)).toEqual([3]);
+    expect(extractLinkedIssues("Closes owner/repo#42", repo)).toEqual([42]);
+    expect(extractLinkedIssues("Fixes Owner/Repo#7", repo)).toEqual([7]);
+    // Bare `#N` without a closing keyword does not link (server parity).
+    expect(extractLinkedIssues("see #7", repo)).toEqual([]);
+    // A different repo's qualified reference must not spoof a same-repo link (#3862).
+    expect(extractLinkedIssues("Resolves other/repo#99", repo)).toEqual([]);
     // Regression: a closing keyword embedded in a longer word must NOT capture a trailing number.
-    expect(extractLinkedIssues("hotfix 5")).toEqual([]);
-    expect(extractLinkedIssues("prefixes 12")).toEqual([]);
-    expect(extractLinkedIssues("unclosed 9")).toEqual([]);
-    expect(extractLinkedIssues("no references here")).toEqual([]);
+    expect(extractLinkedIssues("hotfix 5", repo)).toEqual([]);
+    expect(extractLinkedIssues("prefixes 12", repo)).toEqual([]);
+    expect(extractLinkedIssues("unclosed 9", repo)).toEqual([]);
+    expect(extractLinkedIssues("no references here", repo)).toEqual([]);
+    // REGRESSION (#4039): ignore closing keywords inside inline code spans (PR template checklist example).
+    const templateLine =
+      "- [ ] I linked a currently open issue this PR resolves (e.g. `Closes #123`) — a linked open issue is required for every contributor PR.";
+    expect(extractLinkedIssues(templateLine, repo)).toEqual([]);
+    expect(extractLinkedIssues(`Closes #42\n\n${templateLine}`, repo)).toEqual([42]);
   });
 
   it("parses remotes, changed-file stats, linked issues, and refuses source upload mode", async () => {
diff --git a/test/unit/predicted-gate-engine-branch-coverage.test.ts b/test/unit/predicted-gate-engine-branch-coverage.test.ts
index afad05107e..eadebc5fa4 100644
--- a/test/unit/predicted-gate-engine-branch-coverage.test.ts
+++ b/test/unit/predicted-gate-engine-branch-coverage.test.ts
@@ -380,6 +380,10 @@ describe("predicted-gate engine branch coverage (#2283)", () => {
 
     expect(internals.extractLinkedIssueNumbers("closes other/repo#9", REPO.fullName)).not.toContain(9);
     expect(internals.extractLinkedIssueNumbers(`closes ${REPO.fullName}#9`, REPO.fullName)).toContain(9);
+    const templateLine =
+      "- [ ] I linked a currently open issue this PR resolves (e.g. `Closes #123`) — a linked open issue is required for every contributor PR.";
+    expect(internals.extractLinkedIssueNumbers(templateLine, REPO.fullName)).toEqual([]);
+    expect(internals.extractLinkedIssueNumbers(`Closes #42\n\n${templateLine}`, REPO.fullName)).toEqual([42]);
 
     const issueQuality: IssueQualityReport = {
       repoFullName: REPO.fullName,