diff --git a/navi/core/container.py b/navi/core/container.py
index b565508..84be58d 100644
--- a/navi/core/container.py
+++ b/navi/core/container.py
@@ -2,10 +2,13 @@
 
 from __future__ import annotations
 
+import structlog
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
 from navi.config import settings
+
+logger = structlog.get_logger()
 from navi.context_providers._loader import ContextProviderRegistry
 from navi.llm.ollama import OllamaBackend
 
@@ -122,15 +125,43 @@
 
     workers = build_default_workers()
 
-    # Callback: register MCP tools whenever a server connects (startup or health-check reconnect)
+    # Register MCP tools for servers that connected during startup.
+    # This must happen AFTER build_default_registries creates tool_registry.
+    for srv_name, client in mcp_manager.clients.items():
+        if not client.connected:
+            continue
+        try:
+            tools = await client.list_tools()
+            logger.info(
+                "Registering startup MCP tools for %r -> %d tools",
+                srv_name, len(tools),
+            )
+            for tool in tools:
+                mcp_tool = McpTool(
+                    server_name=srv_name,
+                    tool_name=tool.name,
+                    description=tool.description or "",
+                    parameters=tool.inputSchema,
+                    manager=mcp_manager,
+                )
+                tool_registry.register_external(mcp_tool)
+        except Exception as exc:
+            logger.warning("Failed to register MCP tools for %r: %s", srv_name, exc)
+
+    # Callback for health-check reconnects (server comes back online later)
     async def _on_mcp_server_connected(server_name: str) -> None:
         from navi.core.event_bus import get_event_bus
         from navi.core.events import McpStatusUpdate
         client = mcp_manager.clients.get(server_name)
         if not client:
+            logger.warning("_on_mcp_server_connected: no client for %r", server_name)
             return
         try:
             tools = await client.list_tools()
+            logger.info(
+                "_on_mcp_server_connected: %r -> %d tools",
+                server_name, len(tools),
+            )
             for tool in tools:
                 mcp_tool = McpTool(
                     server_name=server_name,
@@ -140,6 +171,9 @@
                     manager=mcp_manager,
                 )
                 tool_registry.register_external(mcp_tool)
+                logger.debug(
+                    "Registered MCP tool: %s", mcp_tool.name,
+                )
             await get_event_bus().publish(
                 McpStatusUpdate(
                     server_name=server_name,
diff --git a/navi/core/tool_utils.py b/navi/core/tool_utils.py
index d8821e7..4041b40 100644
--- a/navi/core/tool_utils.py
+++ b/navi/core/tool_utils.py
@@ -1,10 +1,13 @@
 """Tool list construction shared between Agent and SubAgentRunner."""
 
+import logging
 from pathlib import Path
 
 from navi.config import settings
 from navi.tools._internal.base import Tool
 
+log = logging.getLogger(__name__)
+
 _USER_ENABLED_FILE = Path(settings.tools_dir) / "enabled.json"
 
 
@@ -47,9 +50,12 @@
                             names.append(full_name)
 
     result = []
+    missing = []
     for name in names:
         try:
             result.append(tool_registry.get(name))
         except Exception:
-            pass
+            missing.append(name)
+    if missing:
+        log.warning("build_tool_list missing tools: %s", missing)
     return result
diff --git a/navi/mcp/client.py b/navi/mcp/client.py
index 7d10f30..9807441 100644
--- a/navi/mcp/client.py
+++ b/navi/mcp/client.py
@@ -58,10 +58,6 @@
         if self._connected:
             return
 
-        # Ensure any stale transport/session from a prior disconnect or
-        # mark_disconnected() is fully torn down before we open fresh ones.
-        await self._cleanup()
-
         try:
             if self.config.is_stdio:
                 if not self.config.command:
@@ -138,7 +134,6 @@
         Used by the health-check loop when a server drops silently.
         """
         self._connected = False
-        self._session = None
 
     async def _cleanup(self) -> None:
         try: