diff --git a/openhands/integrations/bitbucket/service/repos.py b/openhands/integrations/bitbucket/service/repos.py
index b2ab99e380..5b29742b8d 100644
--- a/openhands/integrations/bitbucket/service/repos.py
+++ b/openhands/integrations/bitbucket/service/repos.py
@@ -13,7 +13,13 @@ class BitBucketReposMixin(BitBucketMixinBase):
     """
 
     async def search_repositories(
-        self, query: str, per_page: int, sort: str, order: str, public: bool
+        self,
+        query: str,
+        per_page: int,
+        sort: str,
+        order: str,
+        public: bool,
+        app_mode: AppMode,
     ) -> list[Repository]:
         """Search for repositories."""
         repositories = []
diff --git a/openhands/integrations/github/service/repos.py b/openhands/integrations/github/service/repos.py
index 89df86fadb..855eb08275 100644
--- a/openhands/integrations/github/service/repos.py
+++ b/openhands/integrations/github/service/repos.py
@@ -161,6 +161,29 @@ class GitHubReposMixin(GitHubMixinBase):
             logger.warning(f'Failed to get user organizations: {e}')
             return []
 
+    async def get_organizations_from_installations(self) -> list[str]:
+        """Get list of organization logins from GitHub App installations.
+
+        This method provides a more reliable way to get organizations that the
+        GitHub App has access to, regardless of user membership context.
+        """
+        try:
+            # Get installations with account details
+            url = f'{self.BASE_URL}/user/installations'
+            response, _ = await self._make_request(url)
+            installations = response.get('installations', [])
+
+            orgs = []
+            for installation in installations:
+                account = installation.get('account', {})
+                if account.get('type') == 'Organization':
+                    orgs.append(account.get('login'))
+
+            return orgs
+        except Exception as e:
+            logger.warning(f'Failed to get organizations from installations: {e}')
+            return []
+
     def _fuzzy_match_org_name(self, query: str, org_name: str) -> bool:
         """Check if query fuzzy matches organization name."""
         query_lower = query.lower().replace('-', '').replace('_', '').replace(' ', '')
@@ -181,7 +204,13 @@ class GitHubReposMixin(GitHubMixinBase):
         return False
 
     async def search_repositories(
-        self, query: str, per_page: int, sort: str, order: str, public: bool
+        self,
+        query: str,
+        per_page: int,
+        sort: str,
+        order: str,
+        public: bool,
+        app_mode: AppMode,
     ) -> list[Repository]:
         url = f'{self.BASE_URL}/search/repositories'
         params = {
@@ -206,9 +235,12 @@ class GitHubReposMixin(GitHubMixinBase):
             query_with_user = f'org:{org} in:name {repo_query}'
             params['q'] = query_with_user
         elif not public:
-            # Expand search scope to include user's repositories and organizations they're a member of
+            # Expand search scope to include user's repositories and organizations the app has access to
             user = await self.get_user()
-            user_orgs = await self.get_user_organizations()
+            if app_mode == AppMode.SAAS:
+                user_orgs = await self.get_organizations_from_installations()
+            else:
+                user_orgs = await self.get_user_organizations()
 
             # Search in user repos and org repos separately
             all_repos = []
diff --git a/openhands/integrations/gitlab/service/repos.py b/openhands/integrations/gitlab/service/repos.py
index 6cfd95b043..78018c3d9d 100644
--- a/openhands/integrations/gitlab/service/repos.py
+++ b/openhands/integrations/gitlab/service/repos.py
@@ -75,6 +75,7 @@ class GitLabReposMixin(GitLabMixinBase):
         sort: str = 'updated',
         order: str = 'desc',
         public: bool = False,
+        app_mode: AppMode = AppMode.OSS,
     ) -> list[Repository]:
         if public:
             # When public=True, query is a GitLab URL that we need to parse
diff --git a/openhands/integrations/provider.py b/openhands/integrations/provider.py
index 16b6e55891..064309e372 100644
--- a/openhands/integrations/provider.py
+++ b/openhands/integrations/provider.py
@@ -294,12 +294,13 @@ class ProviderHandler:
         per_page: int,
         sort: str,
         order: str,
+        app_mode: AppMode,
     ) -> list[Repository]:
         if selected_provider:
             service = self.get_service(selected_provider)
             public = self._is_repository_url(query, selected_provider)
             user_repos = await service.search_repositories(
-                query, per_page, sort, order, public
+                query, per_page, sort, order, public, app_mode
             )
             return self._deduplicate_repositories(user_repos)
 
@@ -309,7 +310,7 @@ class ProviderHandler:
                 service = self.get_service(provider)
                 public = self._is_repository_url(query, provider)
                 service_repos = await service.search_repositories(
-                    query, per_page, sort, order, public
+                    query, per_page, sort, order, public, app_mode
                 )
                 all_repos.extend(service_repos)
             except Exception as e:
diff --git a/openhands/integrations/service_types.py b/openhands/integrations/service_types.py
index 9c22c660a8..cfc4839059 100644
--- a/openhands/integrations/service_types.py
+++ b/openhands/integrations/service_types.py
@@ -458,7 +458,13 @@ class GitService(Protocol):
         ...
 
     async def search_repositories(
-        self, query: str, per_page: int, sort: str, order: str, public: bool
+        self,
+        query: str,
+        per_page: int,
+        sort: str,
+        order: str,
+        public: bool,
+        app_mode: AppMode,
     ) -> list[Repository]:
         """Search for public repositories"""
         ...
diff --git a/openhands/server/routes/git.py b/openhands/server/routes/git.py
index db0f0255b4..753cf6f12f 100644
--- a/openhands/server/routes/git.py
+++ b/openhands/server/routes/git.py
@@ -148,7 +148,7 @@ async def search_repositories(
         )
         try:
             repos: list[Repository] = await client.search_repositories(
-                selected_provider, query, per_page, sort, order
+                selected_provider, query, per_page, sort, order, server_config.app_mode
             )
             return repos
 
diff --git a/tests/unit/integrations/bitbucket/test_bitbucket_repos.py b/tests/unit/integrations/bitbucket/test_bitbucket_repos.py
index 5d8dc630d5..dc7d01c6ac 100644
--- a/tests/unit/integrations/bitbucket/test_bitbucket_repos.py
+++ b/tests/unit/integrations/bitbucket/test_bitbucket_repos.py
@@ -8,6 +8,7 @@ from pydantic import SecretStr
 from openhands.integrations.bitbucket.bitbucket_service import BitBucketService
 from openhands.integrations.service_types import OwnerType, Repository
 from openhands.integrations.service_types import ProviderType as ServiceProviderType
+from openhands.server.types import AppMode
 
 
 @pytest.fixture
@@ -37,7 +38,12 @@ async def test_search_repositories_url_parsing_standard_url(bitbucket_service):
     ) as mock_get_repo:
         url = 'https://bitbucket.org/workspace/repo'
         repositories = await bitbucket_service.search_repositories(
-            query=url, per_page=10, sort='updated', order='desc', public=True
+            query=url,
+            per_page=10,
+            sort='updated',
+            order='desc',
+            public=True,
+            app_mode=AppMode.OSS,
         )
 
         # Verify the correct workspace/repo combination was extracted and passed
@@ -70,7 +76,12 @@ async def test_search_repositories_url_parsing_with_extra_path_segments(
         # Test complex URL with query params, fragments, and extra paths
         url = 'https://bitbucket.org/my-workspace/my-repo/src/feature-branch/src/main.py?at=feature-branch&fileviewer=file-view-default#lines-25'
         repositories = await bitbucket_service.search_repositories(
-            query=url, per_page=10, sort='updated', order='desc', public=True
+            query=url,
+            per_page=10,
+            sort='updated',
+            order='desc',
+            public=True,
+            app_mode=AppMode.OSS,
         )
 
         # Verify the correct workspace/repo combination was extracted from complex URL
@@ -87,7 +98,12 @@ async def test_search_repositories_url_parsing_invalid_url(bitbucket_service):
     ) as mock_get_repo:
         url = 'not-a-valid-url'
         repositories = await bitbucket_service.search_repositories(
-            query=url, per_page=10, sort='updated', order='desc', public=True
+            query=url,
+            per_page=10,
+            sort='updated',
+            order='desc',
+            public=True,
+            app_mode=AppMode.OSS,
         )
 
         # Should return empty list for invalid URL and not call API
@@ -105,7 +121,12 @@ async def test_search_repositories_url_parsing_insufficient_path_segments(
     ) as mock_get_repo:
         url = 'https://bitbucket.org/workspace'
         repositories = await bitbucket_service.search_repositories(
-            query=url, per_page=10, sort='updated', order='desc', public=True
+            query=url,
+            per_page=10,
+            sort='updated',
+            order='desc',
+            public=True,
+            app_mode=AppMode.OSS,
         )
 
         # Should return empty list for insufficient path segments and not call API
diff --git a/tests/unit/integrations/github/test_github_service.py b/tests/unit/integrations/github/test_github_service.py
index a60423646e..83ac265ca9 100644
--- a/tests/unit/integrations/github/test_github_service.py
+++ b/tests/unit/integrations/github/test_github_service.py
@@ -277,7 +277,7 @@ async def test_github_search_repositories_with_organizations():
         patch.object(service, 'get_user', return_value=mock_user),
         patch.object(
             service,
-            'get_user_organizations',
+            'get_organizations_from_installations',
             return_value=['All-Hands-AI', 'example-org'],
         ),
         patch.object(
@@ -285,7 +285,12 @@ async def test_github_search_repositories_with_organizations():
         ) as mock_request,
     ):
         repositories = await service.search_repositories(
-            query='openhands', per_page=10, sort='stars', order='desc', public=False
+            query='openhands',
+            per_page=10,
+            sort='stars',
+            order='desc',
+            public=False,
+            app_mode=AppMode.SAAS,
         )
 
         # Verify that separate requests were made for user and each organization