diff --git a/gitnexus/src/server/api.ts b/gitnexus/src/server/api.ts
index d9aa00ae6..59096e5b8 100644
--- a/gitnexus/src/server/api.ts
+++ b/gitnexus/src/server/api.ts
@@ -33,7 +33,7 @@ import { mountMCPEndpoints } from './mcp-http.js';
 import { fork } from 'child_process';
 import { fileURLToPath, pathToFileURL } from 'url';
 import { JobManager } from './analyze-job.js';
-import { extractRepoName, getCloneDir, cloneOrPull } from './git-clone.js';
+import { extractRepoName, extractRepoSlug, getCloneDir, cloneOrPull } from './git-clone.js';
 
 const _require = createRequire(import.meta.url);
 const pkg = _require('../../package.json');
@@ -776,7 +776,9 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
         await fs.rm(storagePath, { recursive: true, force: true }).catch(() => {});
 
         // 2. Delete the cloned repo dir if it lives under ~/.gitnexus/repos/
-        const cloneDir = getCloneDir(entry.name);
+        const cloneDir = getCloneDir(
+          entry.remoteUrl ? extractRepoSlug(entry.remoteUrl) : entry.name,
+        );
         try {
           const stat = await fs.stat(cloneDir);
           if (stat.isDirectory()) {
@@ -1291,7 +1293,8 @@ export const createServer = async (port: number, host: string = '127.0.0.1') =>
           // Clone if URL provided
           if (repoUrl && !repoLocalPath) {
             const repoName = extractRepoName(repoUrl);
-            targetPath = getCloneDir(repoName);
+            const repoSlug = extractRepoSlug(repoUrl);
+            targetPath = getCloneDir(repoSlug);
 
             jobManager.updateJob(job.id, {
               status: 'cloning',
diff --git a/gitnexus/src/server/git-clone.ts b/gitnexus/src/server/git-clone.ts
index 0f7bc2653..b07171f1c 100644
--- a/gitnexus/src/server/git-clone.ts
+++ b/gitnexus/src/server/git-clone.ts
@@ -15,10 +15,51 @@ import { isIP } from 'net';
 export function extractRepoName(url: string): string {
   const cleaned = url.replace(/\/+$/, '');
   const lastSegment = cleaned.split(/[/:]/).pop() || 'unknown';
-  return lastSegment.replace(/\.git$/, '');
+  return lastSegment.replace(/\.git$/i, '');
 }
 
-/** Get the clone target directory for a repo name. */
+const sanitizeClonePathSegment = (segment: string): string => {
+  const sanitized = segment.replace(/[^a-zA-Z0-9._-]/g, '-');
+  return sanitized && sanitized !== '.' && sanitized !== '..' ? sanitized : 'unknown';
+};
+
+/**
+ * Extract an owner-qualified clone slug from an HTTP(S) git URL.
+ *
+ * The server's clone cache must not be keyed only by the repository basename:
+ * different owners can legitimately publish repositories with the same name.
+ * Include the host and path components so those repositories do not silently
+ * reuse each other's cached clone directory.
+ */
+export function extractRepoSlug(url: string): string {
+  let parsed: URL;
+  try {
+    parsed = new URL(url);
+  } catch {
+    return sanitizeClonePathSegment(extractRepoName(url));
+  }
+
+  const rawSegments = parsed.pathname.split('/').filter(Boolean);
+  if (rawSegments.length === 0) {
+    return sanitizeClonePathSegment(extractRepoName(url));
+  }
+
+  rawSegments[rawSegments.length - 1] = rawSegments[rawSegments.length - 1].replace(
+    /\.git$/i,
+    '',
+  );
+  const segments = [parsed.hostname.toLowerCase(), ...rawSegments].map((segment) => {
+    try {
+      return sanitizeClonePathSegment(decodeURIComponent(segment));
+    } catch {
+      return sanitizeClonePathSegment(segment);
+    }
+  });
+
+  return segments.join('/');
+}
+
+/** Get the clone target directory for a repo name or owner-qualified slug. */
 export function getCloneDir(repoName: string): string {
   return path.join(os.homedir(), '.gitnexus', 'repos', repoName);
 }
diff --git a/gitnexus/test/unit/git-clone.test.ts b/gitnexus/test/unit/git-clone.test.ts
index 832f95641..fa4152f85 100644
--- a/gitnexus/test/unit/git-clone.test.ts
+++ b/gitnexus/test/unit/git-clone.test.ts
@@ -1,5 +1,10 @@
 import { describe, it, expect } from 'vitest';
-import { extractRepoName, getCloneDir, validateGitUrl } from '../../src/server/git-clone.js';
+import {
+  extractRepoName,
+  extractRepoSlug,
+  getCloneDir,
+  validateGitUrl,
+} from '../../src/server/git-clone.js';
 
 describe('git-clone', () => {
   describe('extractRepoName', () => {
@@ -24,6 +29,23 @@ describe('git-clone', () => {
     });
   });
 
+  describe('extractRepoSlug', () => {
+    it('keeps the owner path so same-named repositories do not collide', () => {
+      expect(extractRepoSlug('https://github.com/owner-a/my-repo.git')).toBe(
+        'github.com/owner-a/my-repo',
+      );
+      expect(extractRepoSlug('https://github.com/owner-b/my-repo.git')).toBe(
+        'github.com/owner-b/my-repo',
+      );
+    });
+
+    it('keeps nested group paths for non-GitHub hosts', () => {
+      expect(extractRepoSlug('https://gitlab.com/group/subgroup/repo.git')).toBe(
+        'gitlab.com/group/subgroup/repo',
+      );
+    });
+  });
+
   describe('getCloneDir', () => {
     it('returns path under ~/.gitnexus/repos/', () => {
       const dir = getCloneDir('my-repo');
@@ -31,6 +53,18 @@ describe('git-clone', () => {
       expect(dir).toMatch(/repos/);
       expect(dir).toContain('my-repo');
     });
+
+    it('returns distinct paths for owner-qualified clone slugs', () => {
+      const first = getCloneDir(
+        extractRepoSlug('https://github.com/owner-a/shared.git'),
+      );
+      const second = getCloneDir(
+        extractRepoSlug('https://github.com/owner-b/shared.git'),
+      );
+      expect(first).not.toBe(second);
+      expect(first).toContain('owner-a');
+      expect(second).toContain('owner-b');
+    });
   });
 
   describe('validateGitUrl', () => {