Microsoft Copilot Studio - Rovo MCP tools no longer discovered

Question

I’ve been using the Atlassian Rovo MCP Server with Microsoft Copilot Studio via a custom MCP connector. This was working fine over the past couple of months but stopped discovering tools in Copilot Studio suddenly (since around 11th May).
Due to this the published agent is now failing in teams. I deleted all previous connections and then tried to create a new MCP connection but its giving same issue. Multiple people are facing same issue. There are some threads ongoing for same on Atlassian as well. Link here:- https://community.atlassian.com/forums/Atlassian-Remote-MCP-Server/Microsoft-Copilot-Studio-Rovo-MCP-tools-no-longer-discovered/td-p/3233564

Can you please check this on priority and let me know how to fix this issue?

Answer 1

Rovo tools not being discovered indicates that Copilot Studio is no longer seeing any tools exposed by the MCP server, so the agent has nothing to call. Use the following checks and troubleshooting steps that apply to MCP integrations in Copilot Studio and MCP apps generally.

1. Verify the MCP server and manifest
   • Confirm the Rovo MCP server endpoint is running and reachable.
   • Check the plugin/manifest used for the MCP server:
     • Ensure the functions property still lists the expected tools.
     • In the runtimes section, verify:
       • type is the expected MCP runtime (for example RemoteMCPServer).
       • spec.url points to the correct Rovo MCP endpoint.
       • mcp_tool_description correctly references the JSON file or inline tools definition.
       • run_for_functions includes all tool names that should be callable.
   Example structure:

      "runtimes": [
        {
          "type": "RemoteMCPServer",
          "spec": {
            "url": "https://api.contoso.com/mcp",
            "mcp_tool_description": "mcp-tools.json"
          },
          "run_for_functions": [
            "get_widget",
            "create_widget"
          ]
        }
      ]
   

2. Reconnect the MCP server to the agent in Copilot Studio
   • In Copilot Studio, open the affected agent and go to Tools.
   • Remove the existing MCP tool if it is still listed.
   • Add it again using the MCP flow:
     1. Select Add a tool.
     2. Select Model Context Protocol.
     3. Choose the custom MCP connector for the Rovo server.
     4. Re‑authorize the connection (enter required info, API keys, etc.).
     5. Select Add and configure.
   • This ensures Copilot Studio refreshes the tool list from the MCP server.
3. Confirm tools are visible to the model
   • If using a plugin-style manifest, verify tool visibility settings:
     • For MCP apps, _meta.ui.visibility should include model so tools are available to the model.
   • If tools are not visible to the model, they will not appear in the Actions section and will not be triggered from chat.
4. Check for tool discovery issues in Copilot Studio
   • After reconnecting, open the agent test canvas and:
     • Ensure generative orchestration is turned on, as MCP tools require it.
     • Send a prompt that should clearly require a Rovo tool.
   • If no tools appear in the Actions/debug information:
     • Reconfirm the MCP server endpoint and manifest as in step 1.
     • Ensure there are no reference-type inputs or unsupported schema constructs in the Rovo tool definitions, because:
       • Tools with reference-type inputs are filtered out and won’t appear.
       • Enum inputs are treated as strings, so definitions relying on strict enums may behave differently.
       • Tool schemas that use arrays of multiple types can be truncated; adjust such schemas to a single type.
5. Validate MCP transport compatibility
   • Copilot Studio currently supports the Streamable transport type for MCP.
   • If the Rovo server recently changed to use only SSE or an unsupported transport, tools will not be discovered.
   • Ensure the Rovo server is configured to use a supported Streamable transport compatible with Copilot Studio.
6. Recreate the custom connector if applicable
   • If the Rovo MCP server is connected via a Power Apps custom connector:
     • Delete the existing custom connector connection.
     • Recreate the connector and connection, then re-add it as an MCP tool to the agent.
   • This can resolve issues where the connector definition or authentication has drifted from the MCP server’s current behavior.
7. Test with a new agent
   • Create a new test agent in Copilot Studio.
   • Add the same MCP server as a tool using the steps above.
   • If tools still do not appear, this confirms the issue is at the MCP server/manifest or transport layer rather than the specific agent configuration.

If, after these steps, tools still aren’t discovered and multiple tenants are affected, this strongly suggests a change on the Rovo MCP server side (schema, manifest, transport, or visibility) that needs to be addressed by Atlassian. In that case, continue to track the Atlassian community thread and open a support case with Atlassian, providing:

• The MCP manifest.
• The list of tools expected.
• Screenshots of the Copilot Studio Tools page and debug information showing no MCP tools.

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References:

• Troubleshoot MCP apps in Microsoft 365 Copilot
• Extend your agent with Model Context Protocol
• Connect your agent to an existing Model Context Protocol (MCP) server
• Add tools and resources from a Model Context Protocol (MCP) server to your agent
• Troubleshooting Model Context Protocol (MCP) integration
• Manage tools for agents in Microsoft 365 admin center
• Use an MCP tool in Microsoft Copilot Studio (preview)
• Use Microsoft MCP Server for Enterprise from Copilot Studio