diff --git a/src/mcp_manager.py b/src/mcp_manager.py
index 3cddfab..e588a10 100644
--- a/src/mcp_manager.py
+++ b/src/mcp_manager.py
@@ -43,6 +43,8 @@ class McpManager:
         self._sessions: Dict[str, Any] = {}
         # server_id -> exit stack (for cleanup)
         self._stacks: Dict[str, Any] = {}
+        # Tracking updates to tools/connections for RAG indexing
+        self._generation = 0
 
     async def connect_server(
         self,
@@ -57,16 +59,20 @@ class McpManager:
         """Connect to an MCP server via stdio or SSE transport."""
         try:
             if transport == "stdio":
-                return await self._connect_stdio(server_id, name, command, args or [], env or {})
+                res = await self._connect_stdio(server_id, name, command, args or [], env or {})
             elif transport == "sse":
-                return await self._connect_sse(server_id, name, url)
+                res = await self._connect_sse(server_id, name, url)
             else:
                 logger.error(f"Unknown MCP transport: {transport}")
-                return False
+                res = False
+            if res:
+                self._generation += 1
+            return res
         except Exception as e:
             logger.error(f"Failed to connect MCP server {name} ({server_id}): {e}")
             error_message = _format_mcp_connection_error(name, command or "", args or [], e)
             self._connections[server_id] = {"status": "error", "error": error_message, "name": name}
+            self._generation += 1
             return False
 
     async def _connect_stdio(self, server_id: str, name: str, command: str, args: List[str], env: Dict[str, str]) -> bool:
@@ -182,6 +188,7 @@ class McpManager:
         self._sessions.pop(server_id, None)
         self._tools.pop(server_id, None)
         self._connections.pop(server_id, None)
+        self._generation += 1
         logger.info(f"MCP server disconnected: {server_id}")
 
     async def disconnect_all(self):
@@ -387,7 +394,11 @@ class McpManager:
 
     def get_tool_descriptions_for_prompt(self, disabled_map: Optional[Dict[str, set]] = None) -> str:
         """Generate text describing MCP tools for the agent system prompt. Cached."""
-        cache_key = (frozenset((k, frozenset(v)) for k, v in (disabled_map or {}).items()), len(self._tools))
+        cache_key = (
+            frozenset((k, frozenset(v)) for k, v in (disabled_map or {}).items()),
+            len(self._tools),
+            self._generation,
+        )
         if self._cached_prompt_desc is not None and self._cached_prompt_desc_key == cache_key:
             return self._cached_prompt_desc
         tools = self.get_all_tools(disabled_map)
diff --git a/tests/test_mcp_cache_invalidation.py b/tests/test_mcp_cache_invalidation.py
new file mode 100644
index 0000000..3324e92
--- /dev/null
+++ b/tests/test_mcp_cache_invalidation.py
@@ -0,0 +1,71 @@
+"""Regression test: McpManager._generation must bust the tool prompt cache
+when a server connects/disconnects with the same tool count.
+
+Before the fix, cache_key was (disabled_map, len(_tools)).  A reconnect that
+preserved the tool count left the stale description in place.  After the fix
+the _generation counter is included so any structural change invalidates it.
+"""
+import asyncio
+
+from src.mcp_manager import McpManager
+
+
+def _make_mgr():
+    return McpManager()
+
+
+def _inject_tools(mgr, server_id: str, tools: list):
+    """Directly populate internal dicts as _connect_stdio would after success."""
+    mgr._tools[server_id] = tools
+    mgr._connections[server_id] = {"status": "connected", "name": server_id}
+
+
+# ---------------------------------------------------------------------------
+# _generation increments on disconnect
+# ---------------------------------------------------------------------------
+
+def test_generation_increments_on_disconnect():
+    mgr = _make_mgr()
+    assert mgr._generation == 0
+    _inject_tools(mgr, "srv1", [{"name": "tool_a"}])
+    mgr._generation += 1  # simulate connect increment
+
+    gen_before = mgr._generation
+    asyncio.run(mgr.disconnect_server("srv1"))
+    assert mgr._generation == gen_before + 1
+
+
+# ---------------------------------------------------------------------------
+# Core cache-invalidation regression: stale description after reconnect
+# ---------------------------------------------------------------------------
+
+def test_prompt_cache_busted_after_disconnect_same_tool_count():
+    """The stale-cache bug: two different servers each have 1 tool.
+    After the first disconnects and the second connects, the cache must
+    reflect the new server's tools, not the old one's description.
+    """
+    mgr = _make_mgr()
+
+    # Connect server A with one tool
+    _inject_tools(mgr, "srv_a", [{"name": "tool_alpha", "description": "Alpha tool",
+                                   "inputSchema": {"type": "object", "properties": {}}}])
+    mgr._generation += 1  # simulated successful connect
+
+    desc_a = mgr.get_tool_descriptions_for_prompt()
+    assert "tool_alpha" in desc_a
+
+    # Disconnect A — same tool count (1) as what follows
+    asyncio.run(mgr.disconnect_server("srv_a"))  # bumps _generation
+
+    # Connect server B with a *different* tool but same count (1)
+    _inject_tools(mgr, "srv_b", [{"name": "tool_beta", "description": "Beta tool",
+                                   "inputSchema": {"type": "object", "properties": {}}}])
+    mgr._generation += 1  # simulated successful connect
+
+    desc_b = mgr.get_tool_descriptions_for_prompt()
+
+    # Without the fix both describe tool_alpha (stale cache hit).
+    assert "tool_beta" in desc_b, (
+        "Cache was not invalidated: got stale description after reconnect"
+    )
+    assert "tool_alpha" not in desc_b