Cannot switch accounts using Rovo MCP

[Kaspanoombro]

Hello,

In vscode, i configured the new MCP:

    "Atlassian": {

            "url": "https://mcp.atlassian.com/v1/mcp",

            "type": "http"

        }

And it works.

The problem is that i have 2 different Atlassian accounts (different projects and different instances) and i cannot switch accounts.

I use the option in VSCode to logout:

• click on More, then disconect from account 
• stop and start using different account
• i authenticate with the second account in the browser
• and gives the error:

2026-01-13 14:39:22.842 [info] Connection state: Error 404 status sending message to https://mcp.atlassian.com/v1/mcp: {"jsonrpc":"2.0","error":{"code":-32001,"message":"Session not found"}}; will retry with new session ID

2026-01-13 14:39:22.842 [error] Failed to set MCP server log level: Canceled: Canceled

Another computer and another user that only has access to the second Atlassian account, is able to access using MCP.

Only me, that i have 2 account cannot make the switch.

I also tried to delete all browser data (cookies and storage) and also go to the Atlassian account, in Connected Apps, and delete the MCP.

Still get the same error.

How to solve this?

Thanks.

[Dr Valeri Colon _Connect Centric_]

@Kaspanoombro  This usually happens because MCP session state is cached in more than one place (VS Code + the MCP extension + local storage), so you end up with a stale session ID after switching accounts, which triggers “Session not found”.

Fixes that typically work:

• Use the correct endpoint: VS Code should point to https://mcp.atlassian.com/v1/sse (not /v1/mcp), per Atlassian’s client setup docs.

• In VS Code, fully remove the account and clear extension storage (Command Palette → “Developer: Reload Window”, then “Extensions: Disable/Enable”, or reinstall the MCP/Atlassian extension).

• Close VS Code, then delete cached auth/session data for the extension (VS Code global storage folder), and re-auth in a fresh browser profile.

If it still persists, share the client name/version + the exact setup guide you followed and open a support ticket—this looks like an account-switch bug rather than permissions.

[Marc -Devoteam-]

HI @Kaspanoombro 

Si this on the same Atlassian Instance that you have 2 accounts?

I don't think this is possible.

Can you try a different browser, to use with the second account?

[Kaspanoombro]

No, different URLs. 

[Kaspanoombro]

i deleted cache, cookies, storage in the browser, authenticated with the second account but the MCP still connects to the first account (even after stop/start/disconnect/connect account)....

[Kaspanoombro]

apparently it is a reported issue:
https://github.com/atlassian/atlassian-mcp-server/issues/23