diff --git a/src/resources/extensions/gsd/auto.ts b/src/resources/extensions/gsd/auto.ts
index 264738921..47a233407 100644
--- a/src/resources/extensions/gsd/auto.ts
+++ b/src/resources/extensions/gsd/auto.ts
@@ -48,7 +48,7 @@ import {
   validateCompleteBoundary,
   formatValidationIssues,
 } from "./observability-validator.js";
-import { ensureGitignore } from "./gitignore.js";
+import { ensureGitignore, untrackRuntimeFiles } from "./gitignore.js";
 import { runGSDDoctor, rebuildState } from "./doctor.js";
 import { snapshotSkills, clearSkillSnapshot } from "./skill-discovery.js";
 import {
@@ -381,6 +381,7 @@ export async function startAuto(
 
   // Ensure .gitignore has baseline patterns
   ensureGitignore(base);
+  untrackRuntimeFiles(base);
 
   // Bootstrap .gsd/ if it doesn't exist
   const gsdDir = join(base, ".gsd");
diff --git a/src/resources/extensions/gsd/gitignore.ts b/src/resources/extensions/gsd/gitignore.ts
index 2886519f6..02e8ea924 100644
--- a/src/resources/extensions/gsd/gitignore.ts
+++ b/src/resources/extensions/gsd/gitignore.ts
@@ -8,6 +8,7 @@
 
 import { join } from "node:path";
 import { existsSync, readFileSync, writeFileSync } from "node:fs";
+import { execSync } from "node:child_process";
 
 /**
  * Patterns that are always correct regardless of project type.
@@ -106,6 +107,32 @@ export function ensureGitignore(basePath: string): boolean {
   return true;
 }
 
+/**
+ * Remove BASELINE_PATTERNS runtime paths from the git index if they are
+ * currently tracked. This fixes repos that started tracking these files
+ * before the .gitignore rule was added — git continues tracking files
+ * already in the index even after .gitignore is updated.
+ *
+ * Only removes from the index (`--cached`), never from disk. Idempotent.
+ */
+export function untrackRuntimeFiles(basePath: string): void {
+  // The GSD runtime paths are the first 7 entries in BASELINE_PATTERNS
+  const runtimePaths = BASELINE_PATTERNS.slice(0, 7);
+
+  for (const pattern of runtimePaths) {
+    // Use -r for directory patterns (trailing slash), strip the slash for the command
+    const target = pattern.endsWith("/") ? pattern.slice(0, -1) : pattern;
+    try {
+      execSync(`git rm -r --cached ${target}`, {
+        cwd: basePath,
+        stdio: ["ignore", "ignore", "ignore"],
+      });
+    } catch {
+      // File not tracked or doesn't exist — expected, ignore
+    }
+  }
+}
+
 /**
  * Ensure basePath/.gsd/PREFERENCES.md exists as an empty template.
  * Creates the file with frontmatter only if it doesn't exist.
diff --git a/src/resources/extensions/gsd/guided-flow.ts b/src/resources/extensions/gsd/guided-flow.ts
index a51bc83a6..df7d12b42 100644
--- a/src/resources/extensions/gsd/guided-flow.ts
+++ b/src/resources/extensions/gsd/guided-flow.ts
@@ -21,7 +21,7 @@ import {
 import { join } from "node:path";
 import { readFileSync, existsSync, mkdirSync, readdirSync, rmSync } from "node:fs";
 import { execSync, execFileSync } from "node:child_process";
-import { ensureGitignore, ensurePreferences } from "./gitignore.js";
+import { ensureGitignore, ensurePreferences, untrackRuntimeFiles } from "./gitignore.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import { showConfirm } from "../shared/confirm-ui.js";
 
@@ -457,6 +457,7 @@ export async function showSmartEntry(
 
   // ── Ensure .gitignore has baseline patterns ──────────────────────────
   ensureGitignore(basePath);
+  untrackRuntimeFiles(basePath);
 
   // ── No GSD project OR no milestone → Create first/next milestone ────
   if (!existsSync(join(basePath, ".gsd"))) {
diff --git a/src/resources/extensions/gsd/tests/git-service.test.ts b/src/resources/extensions/gsd/tests/git-service.test.ts
index 994e7e410..2811db1b1 100644
--- a/src/resources/extensions/gsd/tests/git-service.test.ts
+++ b/src/resources/extensions/gsd/tests/git-service.test.ts
@@ -1,4 +1,4 @@
-import { mkdtempSync, mkdirSync, writeFileSync, rmSync } from "node:fs";
+import { mkdtempSync, mkdirSync, writeFileSync, rmSync, existsSync } from "node:fs";
 import { join, dirname } from "node:path";
 import { tmpdir } from "node:os";
 import { execSync } from "node:child_process";
@@ -1370,6 +1370,58 @@ async function main(): Promise<void> {
     assert(true, "PreMergeCheckResult type exported and usable");
   }
 
+  // ─── untrackRuntimeFiles: removes tracked runtime files from index ───
+
+  console.log("\n=== untrackRuntimeFiles ===");
+
+  {
+    const { untrackRuntimeFiles } = await import("../gitignore.ts");
+    const repo = mkdtempSync(join(tmpdir(), "gsd-untrack-"));
+    run("git init -b main", repo);
+    run("git config user.email test@test.com", repo);
+    run("git config user.name Test", repo);
+
+    // Create and track runtime files (simulates pre-.gitignore state)
+    mkdirSync(join(repo, ".gsd", "activity"), { recursive: true });
+    mkdirSync(join(repo, ".gsd", "runtime"), { recursive: true });
+    writeFileSync(join(repo, ".gsd", "completed-units.json"), '["u1"]');
+    writeFileSync(join(repo, ".gsd", "metrics.json"), '{}');
+    writeFileSync(join(repo, ".gsd", "STATE.md"), "# State");
+    writeFileSync(join(repo, ".gsd", "activity", "log.jsonl"), "{}");
+    writeFileSync(join(repo, ".gsd", "runtime", "data.json"), "{}");
+    writeFileSync(join(repo, "src.ts"), "code");
+    run("git add -A", repo);
+    run("git commit -m init", repo);
+
+    // Precondition: runtime files are tracked
+    const trackedBefore = run("git ls-files .gsd/", repo);
+    assert(trackedBefore.includes("completed-units.json"), "untrack: precondition — completed-units tracked");
+    assert(trackedBefore.includes("metrics.json"), "untrack: precondition — metrics tracked");
+
+    // Run untrackRuntimeFiles
+    untrackRuntimeFiles(repo);
+
+    // Runtime files should be removed from the index
+    const trackedAfter = run("git ls-files .gsd/", repo);
+    assertEq(trackedAfter, "", "untrack: all runtime files removed from index");
+
+    // Non-runtime files remain tracked
+    const srcTracked = run("git ls-files src.ts", repo);
+    assert(srcTracked.includes("src.ts"), "untrack: non-runtime files remain tracked");
+
+    // Files still exist on disk
+    assert(existsSync(join(repo, ".gsd", "completed-units.json")),
+      "untrack: completed-units.json still on disk");
+    assert(existsSync(join(repo, ".gsd", "metrics.json")),
+      "untrack: metrics.json still on disk");
+
+    // Idempotent — running again doesn't error
+    untrackRuntimeFiles(repo);
+    assert(true, "untrack: second call is idempotent (no error)");
+
+    rmSync(repo, { recursive: true, force: true });
+  }
+
   console.log(`\nResults: ${passed} passed, ${failed} failed`);
   if (failed > 0) process.exit(1);
   console.log("All tests passed ✓");