diff --git a/openhands/server/routes/conversation.py b/openhands/server/routes/conversation.py
index 5dd3970efe..7172f29d18 100644
--- a/openhands/server/routes/conversation.py
+++ b/openhands/server/routes/conversation.py
@@ -83,7 +83,7 @@ def _get_v0_conversation_config(
     }
 
 
-@app.get('/config')
+@app.get('/config', deprecated=True)
 async def get_remote_runtime_config(
     conversation_id: str,
     app_conversation_info_service: AppConversationInfoService = app_conversation_info_service_dependency,
@@ -91,6 +91,10 @@ async def get_remote_runtime_config(
 ) -> JSONResponse:
     """Retrieve the runtime configuration.
 
+    .. deprecated::
+        This endpoint is deprecated. The config is now returned as part of
+        GET /api/v1/app-conversation/{conversation_id}. Use that endpoint instead.
+
     For V0 conversations: returns runtime_id and session_id from the runtime.
     For V1 conversations: returns sandbox_id as runtime_id and conversation_id as session_id.
     """
diff --git a/openhands/server/routes/feedback.py b/openhands/server/routes/feedback.py
index 468ff03c61..8a02439047 100644
--- a/openhands/server/routes/feedback.py
+++ b/openhands/server/routes/feedback.py
@@ -24,7 +24,7 @@ app = APIRouter(
 )
 
 
-@app.post('/submit-feedback')
+@app.post('/submit-feedback', deprecated=True)
 async def submit_feedback(
     request: Request, conversation: ServerConversation = Depends(get_conversation)
 ) -> JSONResponse:
@@ -32,6 +32,10 @@ async def submit_feedback(
 
     This function stores the provided feedback data.
 
+    .. deprecated::
+        Submitting feedback in OSS doesn't really make sense. This endpoint is deprecated
+        and will be removed.
+
     To submit feedback:
     ```sh
     curl -X POST -d '{"email": "test@example.com"}' -H "Authorization:"
diff --git a/openhands/server/routes/manage_conversations.py b/openhands/server/routes/manage_conversations.py
index 7f464845b2..1d2661d369 100644
--- a/openhands/server/routes/manage_conversations.py
+++ b/openhands/server/routes/manage_conversations.py
@@ -704,13 +704,18 @@ async def _delete_v0_conversation(conversation_id: str, user_id: str | None) ->
     return True
 
 
-@app.get('/conversations/{conversation_id}/remember-prompt')
+@app.get('/conversations/{conversation_id}/remember-prompt', deprecated=True)
 async def get_prompt(
     event_id: int,
     conversation_id: str = Depends(validate_conversation_id),
     user_settings: SettingsStore = Depends(get_user_settings_store),
     metadata: ConversationMetadata = Depends(get_conversation_metadata),
 ):
+    """Get the remember prompt for the microagent UI.
+
+    .. deprecated::
+        This endpoint is deprecated. Microagent UI is deprecated in V1.
+    """
     # get event store for the conversation
     event_store = EventStore(
         sid=conversation_id, file_store=file_store, user_id=metadata.user_id
@@ -1467,7 +1472,7 @@ def _create_combined_page_id(
     return base64.b64encode(json.dumps(next_page_data).encode()).decode()
 
 
-@app.get('/microagent-management/conversations')
+@app.get('/microagent-management/conversations', deprecated=True)
 async def get_microagent_management_conversations(
     selected_repository: str,
     page_id: str | None = None,
@@ -1478,6 +1483,9 @@ async def get_microagent_management_conversations(
 ) -> ConversationInfoResultSet:
     """Get conversations for the microagent management page with pagination support.
 
+    .. deprecated::
+        This endpoint is deprecated. Microagent UI is deprecated in V1.
+
     This endpoint returns conversations with conversation_trigger = 'microagent_management'
     and only includes conversations with active PRs. Pagination is supported.
 
diff --git a/openhands/server/routes/public.py b/openhands/server/routes/public.py
index 49dab2f36c..6c8067f87c 100644
--- a/openhands/server/routes/public.py
+++ b/openhands/server/routes/public.py
@@ -36,10 +36,14 @@ async def get_litellm_models(
     return models
 
 
-@app.get('/agents', response_model=list[str])
+@app.get('/agents', response_model=list[str], deprecated=True)
 async def get_agents() -> list[str]:
     """Get all agents supported by LiteLLM.
 
+    .. deprecated::
+        This endpoint is deprecated. The agent definitions are now part of the
+        OpenAPI schema so this is no longer required.
+
     To get the agents:
     ```sh
     curl http://localhost:3000/api/agents
@@ -51,10 +55,14 @@ async def get_agents() -> list[str]:
     return sorted(Agent.list_agents())
 
 
-@app.get('/security-analyzers', response_model=list[str])
+@app.get('/security-analyzers', response_model=list[str], deprecated=True)
 async def get_security_analyzers() -> list[str]:
     """Get all supported security analyzers.
 
+    .. deprecated::
+        This endpoint is deprecated. The security analyzers are now part of the
+        OpenAPI schema so this is no longer required.
+
     To get the security analyzers:
     ```sh
     curl http://localhost:3000/api/security-analyzers
diff --git a/openhands/server/routes/trajectory.py b/openhands/server/routes/trajectory.py
index 6fd8685fdc..5a87ea118a 100644
--- a/openhands/server/routes/trajectory.py
+++ b/openhands/server/routes/trajectory.py
@@ -24,12 +24,16 @@ app = APIRouter(
 )
 
 
-@app.get('/trajectory')
+@app.get('/trajectory', deprecated=True)
 async def get_trajectory(
     metadata: ConversationMetadata = Depends(get_conversation_metadata),
 ) -> JSONResponse:
     """Get trajectory.
 
+    .. deprecated::
+        This endpoint is deprecated. Use the V1 endpoint
+        ``GET /app-conversation/{conversation_id}/download`` instead.
+
     This function retrieves the current trajectory and returns it.
     Uses the local EventStore which reads events from the file store,
     so it works with both standalone and nested conversation managers.