diff --git a/apps/web/src/lib/cloud-agent/github-integration-helpers.test.ts b/apps/web/src/lib/cloud-agent/github-integration-helpers.test.ts
index 9ffe3fd474..3119a616e6 100644
--- a/apps/web/src/lib/cloud-agent/github-integration-helpers.test.ts
+++ b/apps/web/src/lib/cloud-agent/github-integration-helpers.test.ts
@@ -232,7 +232,7 @@ describe('github-integration-helpers', () => {
       ]);
     });
 
-    it('lists a repository shared by two installations exactly once, from the primary installation', async () => {
+    it('lists a repository shared by two installations exactly once, preferring the owning installation', async () => {
       mockGetIntegrationsByOrganization.mockResolvedValue([
         buildIntegration({
           id: 'integration-1',
@@ -261,14 +261,101 @@ describe('github-integration-helpers', () => {
         expect.objectContaining({
           fullName: 'acme-core/api',
           platformIntegrationId: 'integration-1',
+          platformAccountLogin: 'acme-core',
         }),
         expect.objectContaining({
           fullName: 'acme-core/shared',
           platformIntegrationId: 'integration-1',
+          platformAccountLogin: 'acme-core',
         }),
         expect.objectContaining({
           fullName: 'acme-labs/scanner',
           platformIntegrationId: 'integration-2',
+          platformAccountLogin: 'acme-labs',
+        }),
+      ]);
+    });
+
+    it('deduplicates a repository reachable through multiple installations, preferring the owning account', async () => {
+      mockGetIntegrationsByOrganization.mockResolvedValue([
+        buildIntegration({
+          id: 'integration-1',
+          platform_installation_id: 'installation-1',
+          platform_account_login: 'alice',
+          repositories: [
+            { id: 1, name: 'api', full_name: 'acme/api', private: true },
+            { id: 2, name: 'docs', full_name: 'acme/docs', private: false },
+          ],
+        }),
+        buildIntegration({
+          id: 'integration-2',
+          platform_installation_id: 'installation-2',
+          platform_account_login: 'acme',
+          repositories: [
+            { id: 1, name: 'api', full_name: 'acme/api', private: true },
+            { id: 3, name: 'scanner', full_name: 'acme/scanner', private: true },
+          ],
+        }),
+      ]);
+
+      const { fetchAllGitHubRepositoriesForOrganization } =
+        await import('./github-integration-helpers');
+      const result = await fetchAllGitHubRepositoriesForOrganization('org-123');
+
+      expect(result.repositories).toEqual([
+        expect.objectContaining({
+          fullName: 'acme/api',
+          platformIntegrationId: 'integration-2',
+          platformAccountLogin: 'acme',
+        }),
+        expect.objectContaining({
+          fullName: 'acme/docs',
+          platformIntegrationId: 'integration-1',
+          platformAccountLogin: 'alice',
+        }),
+        expect.objectContaining({
+          fullName: 'acme/scanner',
+          platformIntegrationId: 'integration-2',
+          platformAccountLogin: 'acme',
+        }),
+      ]);
+    });
+
+    it('deduplicates repositories across multiple active installations of the same account, keeping the primary', async () => {
+      // getIntegrationsByOrganization returns installations oldest-first, so the
+      // first entry is the primary installation a session resolves by default.
+      mockGetIntegrationsByOrganization.mockResolvedValue([
+        buildIntegration({
+          id: 'integration-primary',
+          platform_installation_id: 'installation-1',
+          platform_account_login: 'acme',
+          repositories: [
+            { id: 1, name: 'api', full_name: 'acme/api', private: true },
+            { id: 2, name: 'docs', full_name: 'acme/docs', private: false },
+          ],
+        }),
+        buildIntegration({
+          id: 'integration-newer',
+          platform_installation_id: 'installation-2',
+          platform_account_login: 'acme',
+          repositories: [{ id: 1, name: 'api', full_name: 'acme/api', private: true }],
+        }),
+      ]);
+
+      const { fetchAllGitHubRepositoriesForOrganization } =
+        await import('./github-integration-helpers');
+      const result = await fetchAllGitHubRepositoriesForOrganization('org-123');
+
+      expect(result.repositories).toEqual([
+        expect.objectContaining({
+          fullName: 'acme/api',
+          platformIntegrationId: 'integration-primary',
+          platformAccountLogin: 'acme',
+        }),
+        expect.objectContaining({
+          fullName: 'acme/docs',
+          platformIntegrationId: 'integration-primary',
+          platformAccountLogin: 'acme',
         }),
       ]);
     });
diff --git a/apps/web/src/lib/cloud-agent/github-integration-helpers.ts b/apps/web/src/lib/cloud-agent/github-integration-helpers.ts
index 394a55f18f..b85d33a718 100644
--- a/apps/web/src/lib/cloud-agent/github-integration-helpers.ts
+++ b/apps/web/src/lib/cloud-agent/github-integration-helpers.ts
@@ -61,23 +61,6 @@ const missingIntegrationResponse = (message: string): GitHubRepositoriesResult =
   errorMessage: message,
 });
 
-/**
- * A repository can be reachable from more than one installation. Keep the
- * first occurrence: integrations arrive oldest-first, matching the primary
- * installation a session resolves by default.
- */
-const dedupeRepositories = (
-  repositories: GitHubRepositoriesResult['repositories']
-): GitHubRepositoriesResult['repositories'] => {
-  const seen = new Set<string>();
-  return repositories.filter(repo => {
-    const key = repo.fullName.toLowerCase();
-    if (seen.has(key)) return false;
-    seen.add(key);
-    return true;
-  });
-};
-
 export async function getGitHubTokenForOrganization(
   organizationId: string
 ): Promise<string | undefined> {
@@ -216,6 +199,42 @@ export async function fetchAllGitHubRepositoriesForOrganization(
   return fetchRepositoriesForIntegrations(integrations, forceRefresh);
 }
 
+const repositoryOwner = (fullName: string) => {
+  const slash = fullName.indexOf('/');
+  return slash === -1 ? fullName : fullName.slice(0, slash);
+};
+
+/**
+ * Keeps a single entry per repository when the same repo is reachable through
+ * more than one GitHub installation (for example the app is installed on two
+ * accounts that share a repo, or a reinstall left two active installation rows
+ * for the same account). Prefer the installation whose GitHub account owns the
+ * repository so sessions run against the canonical write identity. Otherwise
+ * keep the first entry: `getIntegrationsByOrganization` returns installations
+ * oldest-first, matching the primary installation a session resolves to by
+ * default.
+ */
+function dedupeRepositories(
+  repositories: GitHubRepositoriesResult['repositories']
+): GitHubRepositoriesResult['repositories'] {
+  const byFullName = new Map<string, GitHubRepositoriesResult['repositories'][number]>();
+  for (const repo of repositories) {
+    const key = repo.fullName.toLowerCase();
+    const existing = byFullName.get(key);
+    if (!existing) {
+      byFullName.set(key, repo);
+      continue;
+    }
+    const owner = repositoryOwner(existing.fullName).toLowerCase();
+    const existingIsOwner = (existing.platformAccountLogin ?? '').toLowerCase() === owner;
+    const candidateIsOwner = (repo.platformAccountLogin ?? '').toLowerCase() === owner;
+    if (candidateIsOwner && !existingIsOwner) {
+      byFullName.set(key, repo);
+    }
+  }
+  return [...byFullName.values()];
+}
+
 async function fetchRepositoriesForIntegrations(
   integrations: Awaited<ReturnType<typeof getIntegrationsByOrganization>>,
   forceRefresh: boolean