Microsoft Foundry: Unable to Remove Atlassian Tool & Integration Fails

Hello @Ward Vandale Adm

Thank you for the detailed information and for explaining the troubleshooting already performed.

We understand that you are experiencing two issues with the Atlassian integration in Microsoft Foundry:

1. The existing Atlassian tool cannot be removed from the Foundry project through the portal.
2. The updated custom MCP connection authenticates successfully, but getAccessibleAtlassianResources fails with an access verification error when retrieving the available Confluence resources.

Based on the current Microsoft Foundry MCP documentation, we recommend focusing first on the connection and authorization path, as Foundry uses the configured project connection to provide the MCP server endpoint and authentication details to the tool.

1. Verify that the Atlassian tool is using the new connection

Please verify the connection associated with the Atlassian MCP tool and confirm that it references the updated Atlassian authentication configuration.

Microsoft documents that the project_connection_id stores the MCP server endpoint, authentication selection, and related information. If an endpoint is specified both in the connection and in the tool configuration, the endpoint in the connection is used.

Therefore, successfully authenticating to the Atlassian MCP server separately does not by itself confirm that the Foundry tool is using the same connection, credentials, or OAuth configuration.

2. Verify the OAuth/authentication configuration

If the custom connection uses OAuth, please verify that:

• The authorization URL and token URL are correct.
• The configured scopes match the scopes required by Atlassian.
• The OAuth consent flow has been completed.
• The credentials/token being used by the Foundry connection are valid and have not expired.

Microsoft specifically identifies invalid credentials, expired tokens, incorrect scopes, and missing OAuth consent as causes of MCP authentication/tool-call failures.

Please also confirm that the Atlassian identity has the necessary permissions to access the relevant Confluence resources. Authentication succeeding does not necessarily establish authorization to every Confluence space.

3. Validate the MCP connection independently

Microsoft recommends testing the MCP server directly when troubleshooting MCP connection issues. Please test the updated Atlassian MCP connection and confirm whether getAccessibleAtlassianResources succeeds outside the affected Foundry tool configuration.

If the call succeeds directly but fails through Foundry, this would help isolate the issue to the Foundry tool/connection configuration rather than the Atlassian MCP server itself.

4. Regarding removal of the existing Atlassian tool

Since the portal removal operation is not completing, please provide the following information in private message so that we can investigate the removal issue separately:

• Exact error/message displayed when attempting to remove the tool
• UTC timestamp of the removal attempt
• Foundry project name and region
• Atlassian tool/connection name
• Screenshot of the current tool configuration
• Any request/correlation ID displayed by the portal

At this stage, we would not want to assume that the removal failure is caused by a dependency or a stuck resource state without the actual error from the removal operation.

Please refer this

Connect agents to MCP server endpoints – Microsoft Learn

Set up MCP server authentication – Microsoft Learn

Create and manage a toolbox in Microsoft Foundry – Microsoft Learn

I Hope this helps. Do let me know if you have any further queries.

Thank you!