How to use MCP servers for accessing JIRA on one resource and Confluence on another Resource

[Ravi Gooty]

Hi,

Wanted to use atlassian mcp server to access both JIRA and Confluence via VS Code.

Currently, we have the below:

JIRA accessible on say - https://resource1.atlassian.net/

Confluence accessible on say - https://resource2.atlassian.net/

It seems, that when I try to authorize mcp server, its overriding/caching/resusing and can at a time can access only one resource.

Any inputs in this regard will be greatly appreciated.

[Himanshu Tiwary]

Hi @Ravi Gooty ,
Welcome to the community!!

What you’re seeing is likely a current limitation, not a mistake in your setup. Atlassian’s MCP docs describe connecting to an Atlassian Cloud site and do not document a supported way to keep Jira on one site and Confluence on another site active in a single MCP connection in VS Code.

There is also an Atlassian Community thread asking for multi-site permissions, which says the MCP server is currently only able to get permissions to a single site. That matches the behavior you described, where re-authorizing seems to reuse or overwrite the previous site.

So the practical answer is One MCP connection = one Atlassian site context

If Jira is on resource1.atlassian.net and Confluence is on resource2.atlassian.net, this is not well supported today in one shared VS Code MCP setup

Your best workaround is to use separate MCP configurations / separate VS Code windows / separate profiles, one per site, if your client allows it

Otherwise, you’ll likely need Atlassian to add proper multi-site support

So in one line: this looks like a product limitation today, not a config issue on your side.
Referance doc: https://support.atlassian.com/atlassian-rovo-mcp-server/docs/getting-started-with-the-atlassian-remote-mcp-server/
https://community.atlassian.com/forums/Confluence-questions/Will-it-be-possible-to-setup-permissions-to-multiple-sites-for/qaq-p/3081544
https://support.atlassian.com/atlassian-rovo-mcp-server/docs/getting-started-with-the-atlassian-remote-mcp-server/