diff --git a/enterprise/server/auth/saas_user_auth.py b/enterprise/server/auth/saas_user_auth.py
index 42bdd9f640..72138c268a 100644
--- a/enterprise/server/auth/saas_user_auth.py
+++ b/enterprise/server/auth/saas_user_auth.py
@@ -35,6 +35,7 @@ from storage.user_authorization_store import UserAuthorizationStore
 from storage.user_store import UserStore
 from tenacity import retry, retry_if_exception_type, stop_after_attempt, wait_fixed
 
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import (
     PROVIDER_TOKEN_TYPE,
     ProviderToken,
@@ -43,7 +44,6 @@ from openhands.integrations.provider import (
 from openhands.server.settings import Settings
 from openhands.server.user_auth.user_auth import AuthType, UserAuth
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.settings.settings_store import SettingsStore
 
 token_manager = TokenManager()
 
diff --git a/enterprise/storage/saas_secrets_store.py b/enterprise/storage/saas_secrets_store.py
index 14d1fb524c..9df72241e1 100644
--- a/enterprise/storage/saas_secrets_store.py
+++ b/enterprise/storage/saas_secrets_store.py
@@ -10,10 +10,10 @@ from storage.database import a_session_maker
 from storage.stored_custom_secrets import StoredCustomSecrets
 from storage.user_store import UserStore
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
 from openhands.core.config.openhands_config import OpenHandsConfig
 from openhands.core.logger import openhands_logger as logger
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.secrets.secrets_store import SecretsStore
 
 
 @dataclass
diff --git a/enterprise/storage/saas_settings_store.py b/enterprise/storage/saas_settings_store.py
index e73c3e62ba..44c40b2813 100644
--- a/enterprise/storage/saas_settings_store.py
+++ b/enterprise/storage/saas_settings_store.py
@@ -21,9 +21,9 @@ from storage.user import User
 from storage.user_settings import UserSettings
 from storage.user_store import UserStore
 
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.core.config.openhands_config import OpenHandsConfig
 from openhands.server.settings import Settings
-from openhands.storage.settings.settings_store import SettingsStore
 from openhands.utils.jsonpatch_compat import deep_merge
 from openhands.utils.llm import is_openhands_model
 
diff --git a/openhands/storage/secrets/file_secrets_store.py b/openhands/app_server/secrets/file_secrets_store.py
similarity index 96%
rename from openhands/storage/secrets/file_secrets_store.py
rename to openhands/app_server/secrets/file_secrets_store.py
index 9e9d744424..3c2093cecc 100644
--- a/openhands/storage/secrets/file_secrets_store.py
+++ b/openhands/app_server/secrets/file_secrets_store.py
@@ -3,11 +3,11 @@ from __future__ import annotations
 import json
 from dataclasses import dataclass
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
 from openhands.core.config.openhands_config import OpenHandsConfig
 from openhands.storage import get_file_store
 from openhands.storage.data_models.secrets import Secrets
 from openhands.storage.files import FileStore
-from openhands.storage.secrets.secrets_store import SecretsStore
 from openhands.utils.async_utils import call_sync_from_async
 
 
diff --git a/openhands/app_server/secrets/secrets_router.py b/openhands/app_server/secrets/secrets_router.py
index 97269b7f49..82abb79a9b 100644
--- a/openhands/app_server/secrets/secrets_router.py
+++ b/openhands/app_server/secrets/secrets_router.py
@@ -13,6 +13,7 @@ from openhands.app_server.secrets.secrets_models import (
     CustomSecretPage,
     CustomSecretWithoutValue,
 )
+from openhands.app_server.secrets.secrets_store import SecretsStore
 from openhands.app_server.utils.dependencies import get_dependencies
 from openhands.app_server.utils.models import EditResponse
 from openhands.integrations.provider import (
@@ -30,7 +31,6 @@ from openhands.server.user_auth import (
     get_secrets_store,
 )
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.secrets.secrets_store import SecretsStore
 
 # Create router with /api/v1/secrets prefix
 router = APIRouter(
diff --git a/openhands/storage/secrets/secrets_store.py b/openhands/app_server/secrets/secrets_store.py
similarity index 100%
rename from openhands/storage/secrets/secrets_store.py
rename to openhands/app_server/secrets/secrets_store.py
diff --git a/openhands/storage/settings/file_settings_store.py b/openhands/app_server/settings/file_settings_store.py
similarity index 96%
rename from openhands/storage/settings/file_settings_store.py
rename to openhands/app_server/settings/file_settings_store.py
index 66820fb5cc..361c91becc 100644
--- a/openhands/storage/settings/file_settings_store.py
+++ b/openhands/app_server/settings/file_settings_store.py
@@ -3,11 +3,11 @@ from __future__ import annotations
 import json
 from dataclasses import dataclass
 
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.core.config.openhands_config import OpenHandsConfig
 from openhands.storage import get_file_store
 from openhands.storage.data_models.settings import Settings
 from openhands.storage.files import FileStore
-from openhands.storage.settings.settings_store import SettingsStore
 from openhands.utils.async_utils import call_sync_from_async
 
 
diff --git a/openhands/app_server/settings/settings_router.py b/openhands/app_server/settings/settings_router.py
index 90b556ea8f..4163cb5992 100644
--- a/openhands/app_server/settings/settings_router.py
+++ b/openhands/app_server/settings/settings_router.py
@@ -9,6 +9,8 @@ from typing import Any
 from fastapi import APIRouter, Depends, status
 from fastapi.responses import JSONResponse
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.app_server.utils.dependencies import get_dependencies
 from openhands.core.logger import openhands_logger as logger
 from openhands.integrations.provider import (
@@ -28,8 +30,6 @@ from openhands.server.user_auth import (
 )
 from openhands.storage.data_models.secrets import Secrets
 from openhands.storage.data_models.settings import Settings
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.settings_store import SettingsStore
 from openhands.utils.llm import (
     get_provider_api_base,
     is_openhands_model,
diff --git a/openhands/storage/settings/settings_store.py b/openhands/app_server/settings/settings_store.py
similarity index 100%
rename from openhands/storage/settings/settings_store.py
rename to openhands/app_server/settings/settings_store.py
diff --git a/openhands/server/config/server_config.py b/openhands/server/config/server_config.py
index 25caa8d5ee..2ca48453a3 100644
--- a/openhands/server/config/server_config.py
+++ b/openhands/server/config/server_config.py
@@ -22,10 +22,10 @@ class ServerConfig(ServerConfigInterface):
     hide_llm_settings = os.environ.get('HIDE_LLM_SETTINGS', 'false') == 'true'
     # This config is used to hide the microagent management page from the users for now. We will remove this once we release the new microagent management page.
     settings_store_class: str = (
-        'openhands.storage.settings.file_settings_store.FileSettingsStore'
+        'openhands.app_server.settings.file_settings_store.FileSettingsStore'
     )
     secret_store_class: str = (
-        'openhands.storage.secrets.file_secrets_store.FileSecretsStore'
+        'openhands.app_server.secrets.file_secrets_store.FileSecretsStore'
     )
     user_auth_class: str = (
         'openhands.server.user_auth.default_user_auth.DefaultUserAuth'
diff --git a/openhands/server/shared.py b/openhands/server/shared.py
index 994c4685f4..a5e0e44eb8 100644
--- a/openhands/server/shared.py
+++ b/openhands/server/shared.py
@@ -11,14 +11,14 @@ import os
 import socketio
 from dotenv import load_dotenv
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.core.config import load_openhands_config
 from openhands.core.config.openhands_config import OpenHandsConfig
 from openhands.server.config.server_config import ServerConfig, load_server_config
 from openhands.server.types import ServerConfigInterface
 from openhands.storage import get_file_store
 from openhands.storage.files import FileStore
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.settings_store import SettingsStore
 from openhands.utils.import_utils import get_impl
 
 load_dotenv()
diff --git a/openhands/server/user_auth/__init__.py b/openhands/server/user_auth/__init__.py
index d6a4c58e3f..59dc67185a 100644
--- a/openhands/server/user_auth/__init__.py
+++ b/openhands/server/user_auth/__init__.py
@@ -2,12 +2,12 @@ from fastapi import Depends, Request
 from fastapi.security import APIKeyHeader
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import PROVIDER_TOKEN_TYPE
 from openhands.server.settings import Settings
 from openhands.server.user_auth.user_auth import AuthType, get_user_auth
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.settings_store import SettingsStore
 
 
 async def get_provider_tokens(request: Request) -> PROVIDER_TOKEN_TYPE | None:
diff --git a/openhands/server/user_auth/default_user_auth.py b/openhands/server/user_auth/default_user_auth.py
index 70d8e177f4..1fb0cb8a54 100644
--- a/openhands/server/user_auth/default_user_auth.py
+++ b/openhands/server/user_auth/default_user_auth.py
@@ -11,13 +11,13 @@ from dataclasses import dataclass
 from fastapi import Request
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import PROVIDER_TOKEN_TYPE
 from openhands.server import shared
 from openhands.server.settings import Settings
 from openhands.server.user_auth.user_auth import UserAuth
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.settings_store import SettingsStore
 
 
 @dataclass
diff --git a/openhands/server/user_auth/user_auth.py b/openhands/server/user_auth/user_auth.py
index 7ebc94593b..922069d6e7 100644
--- a/openhands/server/user_auth/user_auth.py
+++ b/openhands/server/user_auth/user_auth.py
@@ -14,13 +14,13 @@ from enum import Enum
 from fastapi import Request
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import PROVIDER_TOKEN_TYPE, ProviderHandler
 from openhands.integrations.service_types import UserGitInfo
 from openhands.server.settings import Settings
 from openhands.server.shared import server_config
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.settings_store import SettingsStore
 from openhands.utils.import_utils import get_impl
 
 
diff --git a/openhands/utils/import_utils.py b/openhands/utils/import_utils.py
index 7dc25b918f..108db46fca 100644
--- a/openhands/utils/import_utils.py
+++ b/openhands/utils/import_utils.py
@@ -52,7 +52,7 @@ def get_impl(cls: type[T], impl_name: str | None) -> type[T]:
     Args:
         cls: The base class that defines the interface
         impl_name: Fully qualified name of the implementation class, or None to use the base class
-                  e.g. 'openhands.storage.settings.file_settings_store.FileSettingsStore'
+                  e.g. 'openhands.app_server.settings.file_settings_store.FileSettingsStore'
 
     Returns:
         The implementation class, which is guaranteed to be a subclass of cls
diff --git a/tests/unit/app_server/test_secrets_api.py b/tests/unit/app_server/test_secrets_api.py
index 401a4114ff..78fc7f564f 100644
--- a/tests/unit/app_server/test_secrets_api.py
+++ b/tests/unit/app_server/test_secrets_api.py
@@ -9,6 +9,7 @@ from fastapi import FastAPI
 from fastapi.testclient import TestClient
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.file_secrets_store import FileSecretsStore
 from openhands.app_server.secrets.secrets_router import (
     router as secrets_router,
 )
@@ -19,7 +20,6 @@ from openhands.integrations.provider import (
 )
 from openhands.storage import get_file_store
 from openhands.storage.data_models.secrets import Secrets
-from openhands.storage.secrets.file_secrets_store import FileSecretsStore
 
 
 @pytest.fixture
@@ -45,7 +45,7 @@ def file_secrets_store(temp_dir):
     file_store = get_file_store('local', temp_dir)
     store = FileSecretsStore(file_store)
     with patch(
-        'openhands.storage.secrets.file_secrets_store.FileSecretsStore.get_instance',
+        'openhands.app_server.secrets.file_secrets_store.FileSecretsStore.get_instance',
         AsyncMock(return_value=store),
     ):
         yield store
diff --git a/tests/unit/app_server/test_settings_api.py b/tests/unit/app_server/test_settings_api.py
index d4e7cf9b8c..42a822a77a 100644
--- a/tests/unit/app_server/test_settings_api.py
+++ b/tests/unit/app_server/test_settings_api.py
@@ -6,6 +6,9 @@ from fastapi import Request
 from fastapi.testclient import TestClient
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.file_settings_store import FileSettingsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import ProviderToken, ProviderType
 from openhands.integrations.service_types import UserGitInfo
 from openhands.sdk.llm import LLM
@@ -19,9 +22,6 @@ from openhands.server.user_auth.user_auth import UserAuth
 from openhands.storage.data_models.secrets import Secrets
 from openhands.storage.data_models.settings import Settings
 from openhands.storage.memory import InMemoryFileStore
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.file_settings_store import FileSettingsStore
-from openhands.storage.settings.settings_store import SettingsStore
 
 _EXPOSE = {'expose_secrets': True}
 
@@ -103,7 +103,7 @@ def test_client():
             return_value=MockUserAuth(),
         ),
         patch(
-            'openhands.storage.settings.file_settings_store.FileSettingsStore.get_instance',
+            'openhands.app_server.settings.file_settings_store.FileSettingsStore.get_instance',
             AsyncMock(return_value=FileSettingsStore(InMemoryFileStore())),
         ),
     ):
diff --git a/tests/unit/mcp/test_mcp_integration.py b/tests/unit/mcp/test_mcp_integration.py
index 4c2fd439fa..62e84d045a 100644
--- a/tests/unit/mcp/test_mcp_integration.py
+++ b/tests/unit/mcp/test_mcp_integration.py
@@ -4,12 +4,12 @@ from unittest.mock import AsyncMock, patch
 
 import pytest
 
+from openhands.app_server.settings.file_settings_store import FileSettingsStore
 from openhands.core.config.mcp_config import MCPConfig, RemoteMCPServer
 from openhands.sdk.llm import LLM
 from openhands.sdk.settings import AgentSettings
 from openhands.server.user_auth.default_user_auth import DefaultUserAuth
 from openhands.storage.data_models.settings import Settings
-from openhands.storage.settings.file_settings_store import FileSettingsStore
 
 
 def _sdk_mcp_config(settings: Settings) -> MCPConfig | None:
diff --git a/tests/unit/server/routes/test_skills_api.py b/tests/unit/server/routes/test_skills_api.py
index b1daa1bee0..47940c86d4 100644
--- a/tests/unit/server/routes/test_skills_api.py
+++ b/tests/unit/server/routes/test_skills_api.py
@@ -7,15 +7,15 @@ from fastapi import Request
 from fastapi.testclient import TestClient
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.file_settings_store import FileSettingsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import ProviderToken, ProviderType
 from openhands.integrations.service_types import UserGitInfo
 from openhands.server.app import app
 from openhands.server.user_auth.user_auth import UserAuth
 from openhands.storage.data_models.secrets import Secrets
 from openhands.storage.memory import InMemoryFileStore
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.file_settings_store import FileSettingsStore
-from openhands.storage.settings.settings_store import SettingsStore
 
 
 class MockUserAuth(UserAuth):
@@ -75,7 +75,7 @@ def test_client():
             return_value=MockUserAuth(),
         ),
         patch(
-            'openhands.storage.settings.file_settings_store.FileSettingsStore.get_instance',
+            'openhands.app_server.settings.file_settings_store.FileSettingsStore.get_instance',
             AsyncMock(return_value=FileSettingsStore(InMemoryFileStore())),
         ),
     ):
diff --git a/tests/unit/server/test_openapi_schema_generation.py b/tests/unit/server/test_openapi_schema_generation.py
index 8a3f8ad8f7..feb0dcd884 100644
--- a/tests/unit/server/test_openapi_schema_generation.py
+++ b/tests/unit/server/test_openapi_schema_generation.py
@@ -6,15 +6,15 @@ from fastapi import Request
 from fastapi.testclient import TestClient
 from pydantic import SecretStr
 
+from openhands.app_server.secrets.secrets_store import SecretsStore
+from openhands.app_server.settings.file_settings_store import FileSettingsStore
+from openhands.app_server.settings.settings_store import SettingsStore
 from openhands.integrations.provider import ProviderToken, ProviderType
 from openhands.integrations.service_types import UserGitInfo
 from openhands.server.app import app
 from openhands.server.user_auth.user_auth import UserAuth
 from openhands.storage.data_models.secrets import Secrets
 from openhands.storage.memory import InMemoryFileStore
-from openhands.storage.secrets.secrets_store import SecretsStore
-from openhands.storage.settings.file_settings_store import FileSettingsStore
-from openhands.storage.settings.settings_store import SettingsStore
 
 
 class MockUserAuth(UserAuth):
@@ -71,7 +71,7 @@ def test_client():
             return_value=MockUserAuth(),
         ),
         patch(
-            'openhands.storage.settings.file_settings_store.FileSettingsStore.get_instance',
+            'openhands.app_server.settings.file_settings_store.FileSettingsStore.get_instance',
             AsyncMock(return_value=FileSettingsStore(InMemoryFileStore())),
         ),
     ):
diff --git a/tests/unit/storage/settings/test_file_settings_store.py b/tests/unit/storage/settings/test_file_settings_store.py
index 38500db701..12b093a09f 100644
--- a/tests/unit/storage/settings/test_file_settings_store.py
+++ b/tests/unit/storage/settings/test_file_settings_store.py
@@ -4,12 +4,12 @@ from unittest.mock import MagicMock, patch
 import pytest
 from pydantic import SecretStr
 
+from openhands.app_server.settings.file_settings_store import FileSettingsStore
 from openhands.core.config.openhands_config import OpenHandsConfig
 from openhands.sdk.llm import LLM
 from openhands.sdk.settings import AgentSettings, ConversationSettings
 from openhands.storage.data_models.settings import Settings
 from openhands.storage.files import FileStore
-from openhands.storage.settings.file_settings_store import FileSettingsStore
 
 
 @pytest.fixture
@@ -106,7 +106,7 @@ async def test_get_instance():
     config = OpenHandsConfig(file_store='local', file_store_path='/test/path')
 
     with patch(
-        'openhands.storage.settings.file_settings_store.get_file_store'
+        'openhands.app_server.settings.file_settings_store.get_file_store'
     ) as mock_get_store:
         mock_store = MagicMock(spec=FileStore)
         mock_get_store.return_value = mock_store