diff --git a/src/serena/mcp.py b/src/serena/mcp.py
index e307301..a7f9ea2 100644
--- a/src/serena/mcp.py
+++ b/src/serena/mcp.py
@@ -160,8 +160,12 @@ def create_mcp_server_and_agent(
             return
 
         # Get tool names from process-isolated agent
+        # Tools may change as a result of project activation.
+        # NOTE: While we could pass updated tool information on to the MCP server via the callback, Claude Desktop does not,
+        # unfortunately, query for changed tools. It only queries for changed resources and prompts regularly,
+        # so we need to register all tools at startup, unfortunately.
         try:
-            tool_names = process_agent.get_tool_instances()
+            tool_names = process_agent.get_exposed_tool_names()
         except Exception as e:
             log.error(f"Failed to get tool names from process agent: {e}")
             return
diff --git a/src/serena/process_isolated_agent.py b/src/serena/process_isolated_agent.py
index 543b5ec..741e848 100644
--- a/src/serena/process_isolated_agent.py
+++ b/src/serena/process_isolated_agent.py
@@ -80,8 +80,8 @@ class SerenaAgentWorker:
                 return self._is_language_server_running(request_id)
             elif method == "reset_language_server":
                 return self._reset_language_server(request_id)
-            elif method == "get_tool_instances":
-                return self._get_tool_instances(request_id)
+            elif method == "get_exposed_tool_names":
+                return self._get_exposed_tool_names(request_id)
             else:
                 return {"id": request_id, "error": f"Unknown method: {method}"}
 
@@ -160,7 +160,7 @@ class SerenaAgentWorker:
         except Exception as e:
             return {"id": request_id, "error": str(e), "traceback": traceback.format_exc()}
 
-    def _get_tool_instances(self, request_id: str) -> dict[str, Any]:
+    def _get_exposed_tool_names(self, request_id: str) -> dict[str, Any]:
         """Get exposed tool names for MCP tool creation."""
         if self.agent is None:
             return {"id": request_id, "error": "SerenaAgent not initialized"}
@@ -314,9 +314,14 @@ class ProcessIsolatedSerenaAgent:
         """Reset the language server."""
         self._make_request_with_result("reset_language_server")
 
-    def get_tool_instances(self) -> list[str]:
+    def get_exposed_tool_names(self) -> list[str]:
         """Get tool names for MCP tool creation."""
-        return self._make_request_with_result("get_tool_instances")
+        return self._make_request_with_result("get_exposed_tool_names")
+
+    def get_exposed_tool_instances(self) -> list[ToolInterface]:
+        """Get exposed tool instances for MCP tool creation."""
+        tool_names = self.get_exposed_tool_names()
+        return [ProcessIsolatedTool(self, tool_name) for tool_name in tool_names]
 
     def __enter__(self) -> Self:
         self.start()
diff --git a/test/serena/test_make_tool_process_isolation.py b/test/serena/test_make_tool_process_isolation.py
index f0fdda2..3404aa1 100644
--- a/test/serena/test_make_tool_process_isolation.py
+++ b/test/serena/test_make_tool_process_isolation.py
@@ -141,7 +141,7 @@ class TestMakeToolProcessIsolation:
         # Get tool names from both agents
         regular_active_tools = set(regular_agent.get_active_tool_names())
         regular_all_tools = set(tool.get_name_from_cls() for tool in regular_agent.get_exposed_tool_instances())
-        isolated_tool_names = set(process_isolated_agent.get_tool_instances())
+        isolated_tool_names = set(process_isolated_agent.get_exposed_tool_names())
 
         # The process isolated agent should have all tools (exposed, not just active)
         assert regular_all_tools == isolated_tool_names, (