diff --git a/packages/cli/src/context/core/git.service.ts b/packages/cli/src/context/core/git.service.ts
index 216c5460..82657182 100644
--- a/packages/cli/src/context/core/git.service.ts
+++ b/packages/cli/src/context/core/git.service.ts
@@ -27,6 +27,24 @@ export interface WorktreeEntry {
   head: string | null;
 }
 
+const KTX_MANAGED_GIT_CONFIG_KEY = 'ktx.managed';
+
+type GitDirState = 'absent' | 'directory' | 'foreign';
+
+class KtxForeignGitRepositoryError extends Error {
+  constructor(configDir: string) {
+    super(
+      `${configDir} is already a git repository that ktx did not create. ` +
+        'ktx maintains its context in a repository it owns; run ktx in a dedicated directory or move the existing repository aside.',
+    );
+    this.name = 'KtxForeignGitRepositoryError';
+  }
+}
+
+function isNodeErrnoException(error: unknown): error is NodeJS.ErrnoException {
+  return error instanceof Error && 'code' in error;
+}
+
 export type SquashMergeResult =
   | { ok: true; squashSha: string; touchedPaths: string[] }
   | { ok: false; conflict: true; conflictPaths: string[] };
@@ -96,14 +114,42 @@ export class GitService {
     await this.initialize();
   }
 
+  private async gitDirState(): Promise<GitDirState> {
+    try {
+      const stat = await fs.lstat(join(this.configDir, '.git'));
+      return stat.isDirectory() ? 'directory' : 'foreign';
+    } catch (error) {
+      if (isNodeErrnoException(error) && error.code === 'ENOENT') {
+        return 'absent';
+      }
+      throw error;
+    }
+  }
+
+  private async hasKtxManagedMarker(): Promise<boolean> {
+    try {
+      const value = await this.git.raw(['config', '--local', '--get', KTX_MANAGED_GIT_CONFIG_KEY]);
+      return value.trim() === 'true';
+    } catch {
+      return false;
+    }
+  }
+
   private async initialize(): Promise<void> {
     try {
-      // Check if already initialized
-      const isRepo = await this.git.checkIsRepo();
+      const gitDirState = await this.gitDirState();
 
-      if (!isRepo) {
+      if (gitDirState === 'absent') {
         await this.git.init();
-        this.logger.log('Initialized git repository');
+        await this.git.addConfig(KTX_MANAGED_GIT_CONFIG_KEY, 'true');
+        this.logger.log('Initialized ktx-managed git repository');
+      } else if (gitDirState === 'directory') {
+        const isManaged = await this.hasKtxManagedMarker();
+        if (!isManaged) {
+          throw new KtxForeignGitRepositoryError(this.configDir);
+        }
+      } else {
+        throw new KtxForeignGitRepositoryError(this.configDir);
       }
 
       // Keep any auto-maintenance triggered by writes in-process. Detached maintenance can
diff --git a/packages/cli/test/context/core/git.service.init-identity.test.ts b/packages/cli/test/context/core/git.service.init-identity.test.ts
index 8589d1ed..0b3347a8 100644
--- a/packages/cli/test/context/core/git.service.init-identity.test.ts
+++ b/packages/cli/test/context/core/git.service.init-identity.test.ts
@@ -6,14 +6,10 @@ import { afterEach, beforeEach, describe, expect, it } from 'vitest';
 import type { KtxCoreConfig } from '../../../src/context/core/config.js';
 import { GitService } from '../../../src/context/core/git.service.js';
 
-// Regression for the production exception "Failed to initialize git repository"
-// (PostHog issue 019ea9df-96d6-7882-98e2-6b892bf9c1ab, ktx 0.10.0, darwin).
-//
-// Repro: the project directory is ALREADY a git repo with no commits (the user ran
-// `git init` first, or ktx is pointed at an empty repo), AND the machine has no configured
-// git identity (a fresh Mac with no ~/.gitconfig). GitService only set the committer identity
-// on the path where it created the repo itself, so the bootstrap commit failed with
-// "Committer identity unknown" and was rethrown opaquely.
+// Regression for bootstrapping a marked ktx repo on a machine with no configured
+// git identity. A foreign pre-existing repo is rejected by the ownership rule;
+// this test covers the still-valid path where the repo is already ktx-managed
+// but has no HEAD yet.
 describe('GitService.initialize without a configured git identity', () => {
   let repoDir: string;
   let homeDir: string;
@@ -61,8 +57,12 @@ describe('GitService.initialize without a configured git identity', () => {
       delete process.env[key];
     }
 
-    // Pre-create an empty repo: checkIsRepo() will be true, but there is no HEAD yet.
     execFileSync('git', ['init'], { cwd: repoDir, env: process.env, stdio: 'ignore' });
+    execFileSync('git', ['config', '--local', 'ktx.managed', 'true'], {
+      cwd: repoDir,
+      env: process.env,
+      stdio: 'ignore',
+    });
   });
 
   afterEach(async () => {
diff --git a/packages/cli/test/context/core/git.service.repo-isolation.test.ts b/packages/cli/test/context/core/git.service.repo-isolation.test.ts
new file mode 100644
index 00000000..c0e8b26a
--- /dev/null
+++ b/packages/cli/test/context/core/git.service.repo-isolation.test.ts
@@ -0,0 +1,108 @@
+import { execFileSync } from 'node:child_process';
+import { mkdir, mkdtemp, readFile, realpath, rm, writeFile } from 'node:fs/promises';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+
+import type { KtxCoreConfig } from '../../../src/context/core/config.js';
+import { GitService } from '../../../src/context/core/git.service.js';
+
+function coreConfig(configDir: string): KtxCoreConfig {
+  return {
+    storage: { configDir, homeDir: configDir },
+    git: {
+      userName: 'Test User',
+      userEmail: 'test@example.com',
+      bootstrapMessage: 'Initialize test config repo',
+      bootstrapAuthor: 'test-system',
+      bootstrapAuthorEmail: 'system@example.com',
+    },
+  };
+}
+
+function git(cwd: string, args: string[]): string {
+  return execFileSync('git', args, {
+    cwd,
+    encoding: 'utf-8',
+    env: {
+      ...process.env,
+      GIT_AUTHOR_NAME: 'Parent User',
+      GIT_AUTHOR_EMAIL: 'parent@example.com',
+      GIT_COMMITTER_NAME: 'Parent User',
+      GIT_COMMITTER_EMAIL: 'parent@example.com',
+    },
+  }).trim();
+}
+
+describe('GitService repository ownership', () => {
+  let tempDir: string;
+
+  beforeEach(async () => {
+    tempDir = await mkdtemp(join(tmpdir(), 'git-service-isolation-'));
+  });
+
+  afterEach(async () => {
+    await rm(tempDir, { recursive: true, force: true });
+  });
+
+  it('creates and commits inside its own repo when nested in an enclosing repo', async () => {
+    const parentDir = join(tempDir, 'parent');
+    const projectDir = join(parentDir, '.ktx-project');
+    await mkdir(projectDir, { recursive: true });
+
+    git(parentDir, ['init']);
+    await writeFile(join(parentDir, 'README.md'), '# Parent\n', 'utf-8');
+    git(parentDir, ['add', 'README.md']);
+    git(parentDir, ['commit', '-m', 'parent baseline']);
+    const parentHeadBefore = git(parentDir, ['rev-parse', 'HEAD']);
+
+    const service = new GitService(coreConfig(projectDir));
+    await service.onModuleInit();
+
+    expect(git(projectDir, ['config', '--local', '--get', 'ktx.managed'])).toBe('true');
+    expect(git(parentDir, ['rev-parse', 'HEAD'])).toBe(parentHeadBefore);
+    expect(await realpath(git(projectDir, ['rev-parse', '--show-toplevel']))).toBe(await realpath(projectDir));
+
+    await writeFile(join(projectDir, 'wiki.md'), '# Wiki\n', 'utf-8');
+    await service.commitFile('wiki.md', 'Add wiki page', 'Test User', 'test@example.com');
+
+    expect(git(parentDir, ['rev-parse', 'HEAD'])).toBe(parentHeadBefore);
+    expect(git(projectDir, ['log', '--oneline', '--max-count=1'])).toContain('Add wiki page');
+    expect(git(parentDir, ['status', '--short'])).toContain('?? .ktx-project/');
+  });
+
+  it('rejects a foreign repo rooted at the project dir', async () => {
+    const projectDir = join(tempDir, 'foreign');
+    await mkdir(projectDir, { recursive: true });
+    git(projectDir, ['init']);
+    const configBefore = await readFile(join(projectDir, '.git', 'config'), 'utf-8');
+
+    const service = new GitService(coreConfig(projectDir));
+
+    await expect(service.onModuleInit()).rejects.toThrow(/already a git repository that ktx did not create/);
+    expect(await readFile(join(projectDir, '.git', 'config'), 'utf-8')).toBe(configBefore);
+  });
+
+  it('rejects a gitfile at the project dir as foreign', async () => {
+    const projectDir = join(tempDir, 'linked-worktree');
+    await mkdir(projectDir, { recursive: true });
+    await writeFile(join(projectDir, '.git'), 'gitdir: ../actual.git\n', 'utf-8');
+
+    const service = new GitService(coreConfig(projectDir));
+
+    await expect(service.onModuleInit()).rejects.toThrow(/already a git repository that ktx did not create/);
+  });
+
+  it('accepts a marked ktx repo and does not create a second bootstrap commit', async () => {
+    const projectDir = join(tempDir, 'owned');
+    const service = new GitService(coreConfig(projectDir));
+    await service.onModuleInit();
+    const before = await service.revParseHead();
+
+    const second = new GitService(coreConfig(projectDir));
+    await second.onModuleInit();
+
+    expect(await second.revParseHead()).toBe(before);
+    expect(git(projectDir, ['config', '--local', '--get', 'ktx.managed'])).toBe('true');
+  });
+});
diff --git a/packages/cli/test/context/core/git.service.test.ts b/packages/cli/test/context/core/git.service.test.ts
index 8b19ed09..1318add8 100644
--- a/packages/cli/test/context/core/git.service.test.ts
+++ b/packages/cli/test/context/core/git.service.test.ts
@@ -1,3 +1,4 @@
+import { execFileSync } from 'node:child_process';
 import { mkdtemp, readFile, realpath, rm, writeFile } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
@@ -44,6 +45,11 @@ describe('GitService', () => {
       // beforeEach already ran onModuleInit() against an empty temp dir.
       const head = await service.revParseHead();
       expect(head).toMatch(/^[0-9a-f]{40}$/);
+      const marker = execFileSync('git', ['config', '--local', '--get', 'ktx.managed'], {
+        cwd: tempDir,
+        encoding: 'utf-8',
+      }).trim();
+      expect(marker).toBe('true');
     });
 
     it('does not double-commit when re-initialized', async () => {