Atlassian MCP v2 doesn't appear to allow multiple site connections with single account

Question

Atlassian Rovo Legacy plugin on codex used to allow a single account to access multiple sites. With the new mcp server, it only appears to allow a single site connection per account, and attempting to add a secondary site for the same account results in an error or overwriting the site associated with the account. This heavily limits the ability to use the plugin when I need to access confluence pages from multiple sites (domains).

Rebekka Heilmann (viadee) · Answer

Thanks @Ciro for the mention!

The Teamwork Graph tools should query your whole Organization rather than just one site, so using those you'd still get cross-site data. This is currently being rolled out.

There should be full MCP Support through the API Token route as well now.

Tomislav Tobijas · Answer

@kehaas I can just agree with what you said ☝️ On some accounts, I have access to 20+ sites and switching between them/re-authorizing is a pain…

Note that there's an open feature request, and I believe it's something the team is currently working on, although I'm not sure what the planned release date is: ECO-1259: When using external tools to connect to Atlassian MCP Server, allow multiple cloud site connections/mapping

Cheers,

Tobi

Ciro · Answer

Hi there, This looks like how OAuth works on the Atlassian MCP server, not something wrong on your side. Atlassian's OAuth guide says tokens are "typically consented for a specific cloud ID (site)", and the server checks requests against that cloudId. That would explain why a second site fails or replaces the first one. Two things to try: * API token: tokens aren't bound to a cloudId, so one connection can work across sites, as long as each call passes the right cloudId. An org admin has to enable it first, under Atlassian Administration > Connectors > Atlassian MCP server > Authentication. Some tools aren't available with tokens. * One server entry per site: in Codex config.toml, add a [mcp_servers.] table per site pointing at https://mcp.atlassian.com/v2/mcp, run codex mcp login for each and pick a different site at consent. I haven't tested this one in Codex, so it may not hold two logins for the same URL. Also, v1 won't work as a long-term fallback: Atlassian says existing v1 use starts getting v2 tools on March 1, 2027. A recent Champion article expects MCP OAuth to become Unit-aware, which should help with this: https://community.atlassian.com/forums/discussion/3316744/cross-site-rovo-where-it-stands-and-where-its-going Are your sites in the same organization or in different ones? That changes which route is easier.