diff --git a/gitnexus/src/cli/editor-targets.ts b/gitnexus/src/cli/editor-targets.ts
index 212a4c400..600fde2d9 100644
--- a/gitnexus/src/cli/editor-targets.ts
+++ b/gitnexus/src/cli/editor-targets.ts
@@ -56,7 +56,7 @@ export interface McpJsoncTarget {
 export interface CodexMcpTarget {
   id: 'codex';
   label: string;
-  /** Absolute path to ~/.codex/config.toml. */
+  /** Absolute path to CODEX_HOME/config.toml (default ~/.codex/config.toml). */
   configFile: string;
   /** The TOML table header (without brackets) setup writes / uninstall strips. */
   tomlSection: string;
@@ -100,6 +100,9 @@ export interface EditorTargets {
  * `process.env.HOME` before invoking sees the right locations.
  */
 export function getEditorTargets(home: string = os.homedir()): EditorTargets {
+  const codexHome = process.env.CODEX_HOME
+    ? path.resolve(process.env.CODEX_HOME)
+    : path.join(home, '.codex');
   const mcpJsonc: McpJsoncTarget[] = [
     {
       id: 'cursor',
@@ -166,7 +169,7 @@ export function getEditorTargets(home: string = os.homedir()): EditorTargets {
   const codex: CodexMcpTarget = {
     id: 'codex',
     label: 'Codex',
-    configFile: path.join(home, '.codex', 'config.toml'),
+    configFile: path.join(codexHome, 'config.toml'),
     tomlSection: 'mcp_servers.gitnexus',
   };
 
diff --git a/gitnexus/src/cli/setup.ts b/gitnexus/src/cli/setup.ts
index 88a9eed93..cdb778af5 100644
--- a/gitnexus/src/cli/setup.ts
+++ b/gitnexus/src/cli/setup.ts
@@ -1091,16 +1091,13 @@ async function codexHasHttpMcpEntry(configPath: string): Promise<boolean> {
 }
 
 async function setupCodex(result: SetupResult): Promise<void> {
-  const configuredHome = process.env.CODEX_HOME;
-  const codexDir = configuredHome
-    ? path.resolve(configuredHome)
-    : path.join(os.homedir(), '.codex');
-  if (!configuredHome && !(await dirExists(codexDir))) {
+  const configPath = getEditorTargets().codex.configFile;
+  const codexDir = path.dirname(configPath);
+  if (!process.env.CODEX_HOME && !(await dirExists(codexDir))) {
     result.skipped.push('Codex (not installed)');
     return;
   }
 
-  const configPath = path.join(codexDir, 'config.toml');
   try {
     if (await codexHasHttpMcpEntry(configPath)) {
       result.configured.push('Codex (existing HTTP MCP entry kept)');
diff --git a/gitnexus/test/unit/uninstall.test.ts b/gitnexus/test/unit/uninstall.test.ts
index ad20eb5ca..644ca785f 100644
--- a/gitnexus/test/unit/uninstall.test.ts
+++ b/gitnexus/test/unit/uninstall.test.ts
@@ -23,6 +23,7 @@ describe('uninstallCommand', () => {
   let tempHome: string;
   let originalHome: string | undefined;
   let originalUserProfile: string | undefined;
+  let originalCodexHome: string | undefined;
   let originalSkillsRoot: string | undefined;
   let originalExitCode: typeof process.exitCode;
   let skillsRoot: string;
@@ -35,6 +36,8 @@ describe('uninstallCommand', () => {
 
     originalHome = process.env.HOME;
     originalUserProfile = process.env.USERPROFILE;
+    originalCodexHome = process.env.CODEX_HOME;
+    delete process.env.CODEX_HOME;
     originalSkillsRoot = process.env.GITNEXUS_TEST_SKILLS_ROOT;
     originalExitCode = process.exitCode;
 
@@ -57,6 +60,8 @@ describe('uninstallCommand', () => {
     vi.restoreAllMocks();
     process.env.HOME = originalHome;
     process.env.USERPROFILE = originalUserProfile;
+    if (originalCodexHome === undefined) delete process.env.CODEX_HOME;
+    else process.env.CODEX_HOME = originalCodexHome;
     if (originalSkillsRoot === undefined) delete process.env.GITNEXUS_TEST_SKILLS_ROOT;
     else process.env.GITNEXUS_TEST_SKILLS_ROOT = originalSkillsRoot;
     // The command sets process.exitCode=1 on partial failure; restore it so a
@@ -203,6 +208,28 @@ describe('uninstallCommand', () => {
     expect(result).toContain('command = "other"');
   });
 
+  it('dry-runs and removes only the active CODEX_HOME MCP entry', async () => {
+    const activeHome = path.join(tempHome, 'active-codex');
+    const activeConfig = path.join(activeHome, 'config.toml');
+    const defaultConfig = path.join(tempHome, '.codex', 'config.toml');
+    const activeRaw = '[mcp_servers.gitnexus]\ncommand = "active"\n';
+    const defaultRaw = '[mcp_servers.gitnexus]\ncommand = "default"\n';
+    await fs.mkdir(activeHome);
+    await fs.mkdir(path.dirname(defaultConfig));
+    await fs.writeFile(activeConfig, activeRaw);
+    await fs.writeFile(defaultConfig, defaultRaw);
+    process.env.CODEX_HOME = activeHome;
+
+    const uninstallCommand = await importUninstall();
+    await uninstallCommand();
+    expect(vi.mocked(console.log).mock.calls.flat().join('\n')).toContain(activeConfig);
+    expect(await fs.readFile(activeConfig, 'utf-8')).toBe(activeRaw);
+
+    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);
+  });
+
   it('leaves a corrupt JSON config untouched', async () => {
     const claudeJson = path.join(tempHome, '.claude.json');
     const corrupt = '{ not valid json !!!';