diff --git a/gitnexus/src/cli/editor-targets.ts b/gitnexus/src/cli/editor-targets.ts
index 600fde2d9..f3267aa4b 100644
--- a/gitnexus/src/cli/editor-targets.ts
+++ b/gitnexus/src/cli/editor-targets.ts
@@ -208,10 +208,10 @@ export function getEditorTargets(home: string = os.homedir()): EditorTargets {
       // Codex hooks use Claude Code's exact {hooks: {Event: [...]}} JSON shape
       // and hookSpecificOutput response contract, in a dedicated hooks.json
       // (https://developers.openai.com/codex/hooks).
-      settingsFile: path.join(home, '.codex', 'hooks.json'),
+      settingsFile: path.join(codexHome, 'hooks.json'),
       events: ['PreToolUse', 'PostToolUse'],
       needle: 'gitnexus-hook',
-      scriptDir: path.join(home, '.codex', 'hooks', 'gitnexus'),
+      scriptDir: path.join(codexHome, 'hooks', 'gitnexus'),
     },
     {
       id: 'antigravity',
diff --git a/gitnexus/src/cli/setup.ts b/gitnexus/src/cli/setup.ts
index cdb778af5..33de0ad6b 100644
--- a/gitnexus/src/cli/setup.ts
+++ b/gitnexus/src/cli/setup.ts
@@ -1325,7 +1325,7 @@ async function installOpenCodeSkills(result: SetupResult): Promise<void> {
  * Install global Codex skills to ~/.agents/skills/gitnexus/
  */
 async function installCodexSkills(result: SetupResult): Promise<void> {
-  const codexDir = path.join(os.homedir(), '.codex');
+  const codexDir = path.dirname(getEditorTargets().codex.configFile);
   if (!(await dirExists(codexDir))) return;
 
   const skillsDir = skillTarget('codex').dir;
diff --git a/gitnexus/test/unit/setup.test.ts b/gitnexus/test/unit/setup.test.ts
index 289796342..4f7b098a2 100644
--- a/gitnexus/test/unit/setup.test.ts
+++ b/gitnexus/test/unit/setup.test.ts
@@ -834,6 +834,7 @@ describe('Codex hooks (installClaudeSchemaHooks)', () => {
   let tempHome: string;
   let originalHome: string | undefined;
   let originalUserProfile: string | undefined;
+  let originalCodexHome: string | undefined;
 
   const hooksJsonPath = () => path.join(tempHome, '.codex', 'hooks.json');
 
@@ -843,6 +844,8 @@ describe('Codex hooks (installClaudeSchemaHooks)', () => {
 
     originalHome = process.env.HOME;
     originalUserProfile = process.env.USERPROFILE;
+    originalCodexHome = process.env.CODEX_HOME;
+    delete process.env.CODEX_HOME;
     tempHome = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-codex-hooks-'));
     process.env.HOME = tempHome;
     process.env.USERPROFILE = tempHome;
@@ -858,6 +861,8 @@ describe('Codex hooks (installClaudeSchemaHooks)', () => {
     vi.restoreAllMocks();
     process.env.HOME = originalHome;
     process.env.USERPROFILE = originalUserProfile;
+    if (originalCodexHome === undefined) delete process.env.CODEX_HOME;
+    else process.env.CODEX_HOME = originalCodexHome;
     await fs.rm(tempHome, { recursive: true, force: true });
   });
 
@@ -878,6 +883,28 @@ describe('Codex hooks (installClaudeSchemaHooks)', () => {
     ).resolves.toBeUndefined();
   });
 
+  it('installs hooks and skills for active CODEX_HOME without touching the default home', async () => {
+    const activeHome = path.join(tempHome, 'active-codex');
+    const defaultHooks = hooksJsonPath();
+    await fs.rm(path.join(tempHome, '.codex'), { recursive: true, force: true });
+    await fs.mkdir(activeHome);
+    process.env.CODEX_HOME = activeHome;
+
+    const { setupCommand } = await import('../../src/cli/setup.js');
+    await setupCommand({ codingAgent: 'codex' });
+
+    const hooks = JSON.parse(await fs.readFile(path.join(activeHome, 'hooks.json'), 'utf-8')).hooks;
+    expect(hooks.PreToolUse).toHaveLength(1);
+    expect(hooks.PostToolUse).toHaveLength(1);
+    await expect(
+      fs.access(path.join(activeHome, 'hooks', 'gitnexus', 'gitnexus-hook.cjs')),
+    ).resolves.toBeUndefined();
+    await expect(
+      fs.access(path.join(tempHome, '.agents', 'skills', 'gitnexus-guide', 'SKILL.md')),
+    ).resolves.toBeUndefined();
+    await expect(fs.access(defaultHooks)).rejects.toThrow();
+  });
+
   it('is idempotent — a second setup run adds no duplicate entries', async () => {
     const { setupCommand } = await import('../../src/cli/setup.js');
     await setupCommand();
diff --git a/gitnexus/test/unit/uninstall.test.ts b/gitnexus/test/unit/uninstall.test.ts
index 644ca785f..5c3a2e285 100644
--- a/gitnexus/test/unit/uninstall.test.ts
+++ b/gitnexus/test/unit/uninstall.test.ts
@@ -212,22 +212,46 @@ describe('uninstallCommand', () => {
     const activeHome = path.join(tempHome, 'active-codex');
     const activeConfig = path.join(activeHome, 'config.toml');
     const defaultConfig = path.join(tempHome, '.codex', 'config.toml');
+    const activeHooks = path.join(activeHome, 'hooks.json');
+    const defaultHooks = path.join(tempHome, '.codex', 'hooks.json');
+    const activeScriptDir = path.join(activeHome, 'hooks', 'gitnexus');
+    const defaultScriptDir = path.join(tempHome, '.codex', 'hooks', 'gitnexus');
     const activeRaw = '[mcp_servers.gitnexus]\ncommand = "active"\n';
     const defaultRaw = '[mcp_servers.gitnexus]\ncommand = "default"\n';
+    const hooksRaw = JSON.stringify({
+      hooks: {
+        PreToolUse: [
+          { matcher: 'Bash', hooks: [{ type: 'command', command: 'node gitnexus-hook.cjs' }] },
+          { matcher: 'Read', hooks: [{ type: 'command', command: 'user-hook' }] },
+        ],
+      },
+    });
     await fs.mkdir(activeHome);
     await fs.mkdir(path.dirname(defaultConfig));
+    await fs.mkdir(activeScriptDir, { recursive: true });
+    await fs.mkdir(defaultScriptDir, { recursive: true });
     await fs.writeFile(activeConfig, activeRaw);
     await fs.writeFile(defaultConfig, defaultRaw);
+    await fs.writeFile(activeHooks, hooksRaw);
+    await fs.writeFile(defaultHooks, hooksRaw);
     process.env.CODEX_HOME = activeHome;
 
     const uninstallCommand = await importUninstall();
     await uninstallCommand();
     expect(vi.mocked(console.log).mock.calls.flat().join('\n')).toContain(activeConfig);
+    expect(vi.mocked(console.log).mock.calls.flat().join('\n')).toContain(activeHooks);
     expect(await fs.readFile(activeConfig, 'utf-8')).toBe(activeRaw);
+    expect(await fs.readFile(activeHooks, 'utf-8')).toBe(hooksRaw);
 
     await uninstallCommand({ force: true });
     expect(await fs.readFile(activeConfig, 'utf-8')).not.toContain('[mcp_servers.gitnexus]');
     expect(await fs.readFile(defaultConfig, 'utf-8')).toBe(defaultRaw);
+    const remaining = JSON.parse(await fs.readFile(activeHooks, 'utf-8'));
+    expect(remaining.hooks.PreToolUse).toHaveLength(1);
+    expect(remaining.hooks.PreToolUse[0].hooks[0].command).toBe('user-hook');
+    expect(await fs.readFile(defaultHooks, 'utf-8')).toBe(hooksRaw);
+    await expect(fs.access(activeScriptDir)).rejects.toThrow();
+    await expect(fs.access(defaultScriptDir)).resolves.toBeUndefined();
   });
 
   it('leaves a corrupt JSON config untouched', async () => {