To connect your Cline AI agent to a local MCP server, you'll need to configure it using the STDIO transport method, which is designed specifically for local servers running on your machine[1].
Cline stores all MCP server settings in a file called cline_mcp_settings.json
[1]. This file uses a JSON format with an mcpServers
object containing your server configurations.
Here's the typical structure for connecting to a local MCP server:
{
"mcpServers": {
"your-server-name": {
"command": "python",
"args": ["/path/to/your/server.py"],
"env": {
"API_KEY": "your_api_key"
},
"alwaysAllow": ["tool1", "tool2"],
"disabled": false
}
}
}
command
: The executable command to run your local server (e.g.,"python"
,"node"
,"npx"
)args
: Array of arguments passed to the command, typically including the path to your server script
env
: Environment variables to inject into the server process (useful for API keys or configuration)alwaysAllow
: Array of tool names that should be automatically allowed without confirmationdisabled
: Boolean to enable/disable the server (defaults tofalse
)
{
"mcpServers": {
"my-python-server": {
"command": "python",
"args": ["/path/to/server.py"],
"env": {
"DATABASE_URL": "sqlite:///local.db"
}
}
}
}
{
"mcpServers": {
"my-node-server": {
"command": "node",
"args": ["/path/to/server.js"],
"env": {
"PORT": "3000"
}
}
}
}
{
"mcpServers": {
"sqlite-server": {
"command": "npx",
"args": ["-y", "mcp-sqlite", "/path/to/database.db"]
}
}
}
You can also configure MCP servers through Cline's interface[1]:
- Click the MCP Servers icon in the top navigation bar
- Select the "Installed" tab
- Click "Configure MCP Servers" at the bottom
- Add your server configuration through the UI
You can set the maximum response time for MCP server tool calls using the Network Timeout dropdown, with options ranging from 30 seconds to 1 hour (default is 1 minute)[1].
Cline allows you to restrict or disable MCP server functionality entirely using the Cline>Mcp:Mode
setting[1].
- Use absolute paths for your server executables and scripts
- Set appropriate environment variables for configuration rather than hardcoding values
- Test your server independently before adding it to Cline
- Use the
alwaysAllow
parameter for frequently-used, trusted tools to reduce confirmation prompts
This configuration will enable your Cline AI agent to communicate with your local MCP server using the STDIO transport protocol, allowing seamless integration of your custom tools and capabilities.
[1] https://github.com/lastmile-ai/mcp-agent [2] https://modelcontextprotocol.io/clients [3] https://github.com/mcp-use/mcp-use [4] https://dzone.com/articles/mcp-client-agent-architecture-amp-implementation [5] https://openai.github.io/openai-agents-python/mcp/ [6] https://code.visualstudio.com/docs/copilot/chat/mcp-servers [7] https://docs.mistral.ai/agents/mcp/ [8] https://learn.microsoft.com/en-us/dynamics365/customer-service/administer/configure-ai-agent-to-use-mcp-server [9] https://docs.anthropic.com/en/docs/claude-code/mcp [10] https://dev.to/debs_obrien/building-your-first-mcp-server-a-beginners-tutorial-5fag [11] https://huggingface.co/learn/mcp-course/en/unit1/mcp-clients [12] https://docs.continue.dev/customize/deep-dives/mcp [13] https://www.mcpworld.com/en/detail/4d6d346fbbd6c049cc34b7f719c1b7d3 [14] https://www.pulsemcp.com/posts/introduction-to-fast-agent-mcp-client [15] https://modelcontextprotocol.io/quickstart/user [16] https://www.youtube.com/watch?v=aiH79Q-LGjY [17] https://modelcontextprotocol.io/quickstart/server [18] https://docs.cline.bot/mcp/configuring-mcp-servers [19] https://dev.to/developer_harsh/how-to-build-mcp-servers-and-test-locally-from-scratch-3d4j [20] https://www.reddit.com/r/ClaudeAI/comments/1ll88ay/local_mcp_servers_can_now_be_installed_with_one/
Viewing MCP Server Logs When Cline Manages the Process
You're absolutely right that one of the main benefits of running a standalone terminal server is visibility into logging. When Cline manages the MCP server process (STDIO transport), the logging situation is more limited, but there are several ways to access logs.
Current Limitations
When Cline starts and manages your MCP server process, it does hide the stderr output that contains your server's logs[1]. This is a known limitation that makes debugging more challenging compared to running the server standalone in a terminal.
Available Options for Viewing Logs
1. Cline's Built-in Log Viewer
Cline provides a basic log viewing interface:
However, this interface has limitations and may not show all the detailed logging you'd see in a standalone terminal.
2. MCP Inspector Tool
The MCP Inspector is the most powerful option for viewing real-time logs:
# Launch MCP Inspector to proxy your server npx @modelcontextprotocol/inspector node /path/to/your/server.js
The Inspector provides:
3. File-Based Logging Workaround
Since direct console visibility is limited, many developers implement file-based logging:
Node.js Example:
Python Example:
4. Structured Logging Best Practices
For better visibility regardless of transport method, implement structured logging:
Key Logging Requirements
When implementing logging for MCP servers, remember:
Feature Request Status
There's an active GitHub issue requesting better log visibility in Cline[1]. The community has identified this as a significant debugging limitation, so improved logging support may come in future versions.
Recommendation
For development and debugging, consider this hybrid approach:
While Cline's STDIO transport does limit direct log visibility compared to running standalone servers, these workarounds provide viable alternatives for monitoring and debugging your MCP server's behavior.
[1] cline/cline#1959
[2] https://apidog.com/blog/cline-mcp-servers/
[3] https://www.mcpevals.io/blog/debugging-mcp-servers-tips-and-best-practices
[4] https://modelcontextprotocol.io/docs/tools/inspector
[5] https://modelcontextprotocol.io/docs/tools/debugging
[6] https://modelcontextprotocol.io/specification/2025-03-26/server/utilities/logging
[7] cline/cline#4391
[8] cline/cline#2118
[9] https://snyk.io/articles/how-to-debug-mcp-server-with-anthropic-inspector/
[10] https://www.reddit.com/r/ClaudeAI/comments/1ioxu5r/still_confused_about_how_mcp_works_heres_the/
[11] https://lobehub.com/mcp/hassansaadfr-log-reader-mcp
[12] https://www.ontariomcp.ca/cline-mcp
[13] https://www.youtube.com/watch?v=b5pqTNiuuJg
[14] https://www.datacamp.com/tutorial/cline-ai
[15] https://dev.to/aws/configuring-model-context-protocol-mcp-with-amazon-q-cli-e80
[16] https://www.dynatrace.com/news/blog/mcp-best-practices-cline-live-debugger-developer-experience/
[17] https://code.visualstudio.com/docs/copilot/chat/mcp-servers
[18] https://devblogs.microsoft.com/dotnet/build-a-model-context-protocol-mcp-server-in-csharp/
[19] https://www.observeinc.com/blog/powering-agentic-observability-with-the-observe-mcp-server
[20] https://docs.cline.bot/mcp/mcp-server-development-protocol
[21] cline/cline#1272
[22] https://docs.cline.bot/mcp/mcp-transport-mechanisms
[23] RooCodeInc/Roo-Code#1287
[24] https://www.reddit.com/r/ClaudeAI/comments/1ipvo9k/mcp_servers_work_in_cline_but_fail_in_claude/
[25] https://www.tinybird.co/blog-posts/analyze-mcp-server-usage
[26] https://www.youtube.com/watch?v=98l_k0XYXKs
[27] https://blog.fka.dev/blog/2025-03-25-inspecting-mcp-servers-using-cli/
[28] https://dev.to/aws-builders/implementing-nova-act-mcp-server-on-ecs-fargate-1368
[29] https://mcp-framework.com/docs/debugging/
[30] https://www.youtube.com/watch?v=8MlFALTsUqY
[31] https://github.com/modelcontextprotocol/inspector
[32] continuedev/continue#5736
[33] https://gofastmcp.com/servers/context