diff --git a/.githooks/post-merge b/.githooks/post-merge
new file mode 100755
index 0000000..5c690b5
--- /dev/null
+++ b/.githooks/post-merge
@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ "${MUSAFETY_DISABLE_POST_MERGE_CLEANUP:-0}" == "1" ]]; then
+  exit 0
+fi
+
+repo_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
+if [[ -z "$repo_root" ]]; then
+  exit 0
+fi
+
+branch="$(git -C "$repo_root" rev-parse --abbrev-ref HEAD 2>/dev/null || true)"
+if [[ -z "$branch" || "$branch" == "HEAD" ]]; then
+  exit 0
+fi
+
+base_branch="${MUSAFETY_BASE_BRANCH:-$(git -C "$repo_root" config --get multiagent.baseBranch || true)}"
+if [[ -z "$base_branch" ]]; then
+  base_branch="dev"
+fi
+
+if [[ "$branch" != "$base_branch" ]]; then
+  exit 0
+fi
+
+cli_path="$repo_root/bin/multiagent-safety.js"
+if [[ ! -f "$cli_path" ]]; then
+  exit 0
+fi
+
+node_bin="${MUSAFETY_NODE_BIN:-node}"
+if ! command -v "$node_bin" >/dev/null 2>&1; then
+  exit 0
+fi
+
+"$node_bin" "$cli_path" cleanup \
+  --target "$repo_root" \
+  --base "$base_branch" \
+  --keep-clean-worktrees >/dev/null 2>&1 || true
+
+exit 0
diff --git a/.gitignore b/.gitignore
index ed52393..5ad58bc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,6 +14,7 @@ scripts/install-agent-git-hooks.sh
 scripts/openspec/init-plan-workspace.sh
 .githooks/pre-commit
 .githooks/pre-push
+.githooks/post-merge
 oh-my-codex/
 .codex/skills/guardex/SKILL.md
 .claude/commands/guardex.md
diff --git a/bin/multiagent-safety.js b/bin/multiagent-safety.js
index 5acfaac..01615ac 100755
--- a/bin/multiagent-safety.js
+++ b/bin/multiagent-safety.js
@@ -49,6 +49,7 @@ const TEMPLATE_FILES = [
   'scripts/openspec/init-plan-workspace.sh',
   'githooks/pre-commit',
   'githooks/pre-push',
+  'githooks/post-merge',
   'codex/skills/guardex/SKILL.md',
   'codex/skills/guardex-merge-skills-to-dev/SKILL.md',
   'claude/commands/guardex.md',
@@ -63,6 +64,7 @@ const REQUIRED_WORKFLOW_FILES = [
   'scripts/agent-file-locks.py',
   'scripts/install-agent-git-hooks.sh',
   '.githooks/pre-commit',
+  '.githooks/post-merge',
   '.omx/state/agent-file-locks.json',
 ];
 
@@ -87,12 +89,14 @@ const EXECUTABLE_RELATIVE_PATHS = new Set([
   'scripts/openspec/init-plan-workspace.sh',
   '.githooks/pre-commit',
   '.githooks/pre-push',
+  '.githooks/post-merge',
 ]);
 
 const CRITICAL_GUARDRAIL_PATHS = new Set([
   'AGENTS.md',
   '.githooks/pre-commit',
   '.githooks/pre-push',
+  '.githooks/post-merge',
   'scripts/agent-branch-start.sh',
   'scripts/agent-branch-finish.sh',
   'scripts/agent-worktree-prune.sh',
@@ -118,6 +122,7 @@ const MANAGED_GITIGNORE_PATHS = [
   'scripts/openspec/init-plan-workspace.sh',
   '.githooks/pre-commit',
   '.githooks/pre-push',
+  '.githooks/post-merge',
   'oh-my-codex/',
   '.codex/skills/guardex/SKILL.md',
   '.codex/skills/guardex-merge-skills-to-dev/SKILL.md',
diff --git a/scripts/agent-file-locks.py b/scripts/agent-file-locks.py
index 06cdd7a..53c2d2f 100755
--- a/scripts/agent-file-locks.py
+++ b/scripts/agent-file-locks.py
@@ -27,6 +27,7 @@
     'AGENTS.md',
     '.githooks/pre-commit',
     '.githooks/pre-push',
+    '.githooks/post-merge',
     'scripts/agent-branch-start.sh',
     'scripts/agent-branch-finish.sh',
     'scripts/agent-file-locks.py',
diff --git a/templates/githooks/post-merge b/templates/githooks/post-merge
new file mode 100755
index 0000000..5c690b5
--- /dev/null
+++ b/templates/githooks/post-merge
@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ "${MUSAFETY_DISABLE_POST_MERGE_CLEANUP:-0}" == "1" ]]; then
+  exit 0
+fi
+
+repo_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
+if [[ -z "$repo_root" ]]; then
+  exit 0
+fi
+
+branch="$(git -C "$repo_root" rev-parse --abbrev-ref HEAD 2>/dev/null || true)"
+if [[ -z "$branch" || "$branch" == "HEAD" ]]; then
+  exit 0
+fi
+
+base_branch="${MUSAFETY_BASE_BRANCH:-$(git -C "$repo_root" config --get multiagent.baseBranch || true)}"
+if [[ -z "$base_branch" ]]; then
+  base_branch="dev"
+fi
+
+if [[ "$branch" != "$base_branch" ]]; then
+  exit 0
+fi
+
+cli_path="$repo_root/bin/multiagent-safety.js"
+if [[ ! -f "$cli_path" ]]; then
+  exit 0
+fi
+
+node_bin="${MUSAFETY_NODE_BIN:-node}"
+if ! command -v "$node_bin" >/dev/null 2>&1; then
+  exit 0
+fi
+
+"$node_bin" "$cli_path" cleanup \
+  --target "$repo_root" \
+  --base "$base_branch" \
+  --keep-clean-worktrees >/dev/null 2>&1 || true
+
+exit 0
diff --git a/test/install.test.js b/test/install.test.js
index fa6b2ce..46eec84 100644
--- a/test/install.test.js
+++ b/test/install.test.js
@@ -273,6 +273,7 @@ test('setup provisions workflow files and repo config', () => {
     'scripts/openspec/init-plan-workspace.sh',
     '.githooks/pre-commit',
     '.githooks/pre-push',
+    '.githooks/post-merge',
     '.codex/skills/guardex/SKILL.md',
     '.codex/skills/guardex-merge-skills-to-dev/SKILL.md',
     '.claude/commands/guardex.md',
@@ -320,6 +321,7 @@ test('setup provisions workflow files and repo config', () => {
   assert.match(gitignoreContent, /scripts\/agent-file-locks\.py/);
   assert.match(gitignoreContent, /\.githooks\/pre-commit/);
   assert.match(gitignoreContent, /\.githooks\/pre-push/);
+  assert.match(gitignoreContent, /\.githooks\/post-merge/);
   assert.match(gitignoreContent, /\.omx\//);
   assert.match(gitignoreContent, /oh-my-codex\//);
   assert.match(gitignoreContent, /\.codex\/skills\/guardex\/SKILL\.md/);
@@ -1824,6 +1826,55 @@ test('pre-push blocks codex protected branch pushes even from VS Code Source Con
   assert.match(hookResult.stderr, /\[guardex-preedit-guard\] Codex push detected toward protected branch\./);
 });
 
+test('post-merge auto-runs cleanup on base branch and skips non-base branches', () => {
+  const repoDir = initRepo();
+  seedCommit(repoDir);
+
+  const setupResult = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
+  assert.equal(setupResult.status, 0, setupResult.stderr || setupResult.stdout);
+
+  const markerPath = path.join(repoDir, '.post-merge-cleanup-args');
+  fs.writeFileSync(
+    path.join(repoDir, 'bin', 'multiagent-safety.js'),
+    '#!/usr/bin/env node\n' +
+      "const fs = require('node:fs');\n" +
+      "const marker = process.env.MUSAFETY_POST_MERGE_MARKER;\n" +
+      "if (marker) fs.appendFileSync(marker, process.argv.slice(2).join(' ') + '\\n', 'utf8');\n",
+    'utf8',
+  );
+
+  let result = runCmd('bash', ['.githooks/post-merge', '0'], repoDir, {
+    MUSAFETY_POST_MERGE_MARKER: markerPath,
+  });
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  let invocations = fs
+    .readFileSync(markerPath, 'utf8')
+    .split('\n')
+    .map((line) => line.trim())
+    .filter(Boolean);
+  assert.equal(invocations.length, 1);
+  assert.match(invocations[0], /^cleanup /);
+  assert.match(invocations[0], new RegExp(`--target ${escapeRegexLiteral(repoDir)}`));
+  assert.match(invocations[0], /--base dev/);
+  assert.match(invocations[0], /--keep-clean-worktrees/);
+
+  result = runCmd('git', ['checkout', '-b', 'feature/post-merge-skip'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  result = runCmd('bash', ['.githooks/post-merge', '0'], repoDir, {
+    MUSAFETY_POST_MERGE_MARKER: markerPath,
+  });
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  invocations = fs
+    .readFileSync(markerPath, 'utf8')
+    .split('\n')
+    .map((line) => line.trim())
+    .filter(Boolean);
+  assert.equal(invocations.length, 1, 'post-merge should skip cleanup on non-base branch');
+});
+
 test('codex-agent launches codex inside a fresh sandbox worktree and keeps branch/worktree by default', () => {
   const repoDir = initRepo();
   seedCommit(repoDir);