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How to create a federated connector in M365 Copilot that integrates with Atlassian Rovo MCP

Richard Cho
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August 12, 2026

Has anyone had any luck setting up a custom federated connector in Microsoft Copilot using their docs? https://learn.microsoft.com/en-us/microsoft-365/copilot/connectors/set-up-custom-federated-connectors

Atlassian currently doesn't provide a native MCP connector for Copilot which means admins need to create their own.

I couldn't get past the authentication step. From what I understand, the Atlassian Rovo MCP server uses Oauth 2.1 dynamic client registration which means users don't need to manually create an Oauth app and exchange credentials such as client id, client secret, etc.

I had more luck creating an agent in Copilot but there are some downsides with this approach as users must explicitly mention/tag the agent in the prompt for it to access data in Atlassian whereas a federated connector should just dynamically hook into the prompt.

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Viswanathan Ramachandran
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August 13, 2026

Hi @Richard Cho 

This might of your interest : https://jira.atlassian.com/browse/ECO-1693

Seems a current limitation between how M365 Copilot Custom Federated Connectors and Atlassian Rovo MCP handle authentication:

  • The Problem: M365 Custom Federated Connectors require standard OAuth 2.0 with a static enterprise App Registration (Client ID/Secret, static token endpoints). Atlassian’s Remote MCP server uses OAuth 2.1 Dynamic Client Registration, which breaks the federated connector setup flow at authentication.
  • Why Agents Work: Copilot Studio Agents support Dynamic Discovery auth for MCP endpoints [https://mcp.atlassian.com/v1/mcp] which is why the Agent route works though as you noted, it requires manual mentioning instead of dynamic, passive retrieval across global Copilot prompts.

Workarounds today:

  1. Middleware Proxy: Deploy a small wrapper (e.g., Azure API Management or Azure Function) to translate static OAuth 2.0 requests from M365 into Atlassian’s dynamic authentication flow.
  2. Official Gallery Connector: Wait for Microsoft and Atlassian to release a pre-built connector in the Microsoft 365 Connectors Gallery, which bypasses custom app registration.

You can track feature suggestions for native M365 federated connector support directly on above jira and/or submit feedback on the Microsoft 365 Copilot Feedback Portal.

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