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Trying to integrate with Microsoft Foundry - no success

Sagi Barak_7nb0rf

Hey!

It the new Microsoft Foundry, they allow us to use the Remote MCP of Atlassian.

I'm trying to configure it, but with no success.

This is the configuration panel:

Screenshot 2025-12-10 at 9.40.38 AM.png

I've tried to create an app via the Atlassian developer and input the client id and secret. Also, gave the scopes of read:jira-user, read:jira-work and offline_access.

Then, when trying to give consent, it opens OAuth flow, but I'm getting "Unauthorized" errors afterward.

Did someone got a success to configure it or have an idea how to configure it correctly?

Comments

Dorin_Goldin

Hi Sagi,

No expert but had a bit of struggle myself connecting Atlassian mcp to multiple tools.

2 questions:

1. Do you get the authentication pop up on your browser?

2. Does the mcp url is on the allow list of your company network?

If you have more logs please share them it will be helpful for debugging

Sagi Barak_7nb0rf

Hey!

1. Yes, I did get it.

2. Not sure what you mean by that, but we are using this MCP on other IDEs and apps.

Unfortunately I don't have any other logs, but it doesn't seems to be a network issue. It's something between Atlassian and the Microsoft Foundry directly.

Dorin_Goldin

ok so this is not a network issue for sure - great

did you verify Atlassian mcp supports MS Foundry connection?

Sagi Barak_7nb0rf

They do support Copilot 365 and Azure AI. Azure AI and MS Foundry are not different on the infra.

Also, I've added the relevant domains to the allowed domains on the Rovo MCP settings.

Forefront Helena Foogde

Also trying to achieve this and am wondering if you or anyone else seeing this have manged to succesfully use the official mcp via Microsoft Foundry? I am getting the authentication popup and a "login succesful" but then immediately:

"ErrorAuthentication failed when connecting to the MCP server: https://mcp.atlassian.com:443/v1/sse: Response status code does not indicate success: 401 (Unauthorized).. Verify your authentication headers. Suggestions: First verify the required permissions. If the access token is expired or revoked, recreate the connection. If this connection is shared by other users or workflows, recreate it carefully to avoid disruption."

I have made sure that the scopes set up in Atlassian OAuth are matching the ones i specify in Foundry. Adding the tool in Foundry generated a redirect url that i added as callback url in Atlassian OAuth. However I wasn't quite sure what to put as "refresh url" in the Foundry configuration, I simply pasted "https://auth.atlassian.com/oauth/token" from the "Token url" field. Maybe that was wrong, or does Atlassian MCP not support the Foundry agent yet? Anyone knows?

Matt Parker

I believe I've tried exactly the same as yourself, and face exactly the same issue.

I've tried various approaches with just a single scope, having tried classic and granular too.

We receive the authentication popup and that works, but can't get any further than that.

There is an alternative approach, that can use the JIRA API as a custom integration in Foundry, but that's a bit gnarly as it uses a logic app behind the scenes.

I'll probably raise an issue on https://github.com/atlassian/atlassian-mcp-server

Forefront Helena Foogde

Yes, for now I'm using the logic apps workaround. If the issue with the official MCP is that it's not compatble with Foundry yet it's a bit annoying that that is not made clearer from either Atlassian or Foundry's side...

Georg Fankhauser

Hi there- @Forefront Helena Foogde @Matt Parker

I've stumbled across exactly the same problem (connection and oauth consent work, in playground when beeing incorported ((..)

ErrorAuthentication failed when connecting to the MCP server: https://mcp.atlassian.com:443/v1/sse(..)).

It seems like in the Microsoft Foundry Next Gen the Authentication Workflow is not implemented properly for the current Atlassian Setup.

The Atlassian MCP Server is working with VS Code and we could also facilitate to use with Custom Code and manual Authentication handling => however for productive use, that's not a valid option.

I'll also try to post in other forums on Microsoft side and retry in some weeks.

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