The official Atlassian MCP connector only supports one site at a time and may I know how I can connect multiple Jira sites to Claude using the safest method?
Hi @Buddhika Nanayakkara
The official Atlassian Rovo MCP server (mcp.atlassian.com) uses OAuth 2.1 authorization, which binds the authorized session to a single site during the browser consent flow. But to connect multiple Jira sites safely to Claude without credentials colliding or Claude confusing data between environments, you have two primary methods:
mcp.atlassian.com
If your organization requires using the official hosted Atlassian endpoint with OAuth 2.1 (which enforces enterprise SSO, session policies, and eliminates static API tokens), you can configure multiple named servers in Claude Desktop by giving each instance its own isolated storage directory for OAuth tokens.
Configuration (claude_desktop_config.json) On macOS: ~/Library/Application Support/Claude/claude_desktop_config.json On Windows: %APPDATA%\Claude\claude_desktop_config.json
claude_desktop_config.json
~/Library/Application Support/Claude/claude_desktop_config.json
%APPDATA%\Claude\claude_desktop_config.json
{ "mcpServers": { "jira-production": { "command": "npx", "args": [ "-y", "mcp-remote", "https://mcp.atlassian.com/v1/mcp", "--storage-dir", "/Users/username/.mcp-auth/site-prod" ] }, "jira-sandbox": { "command": "npx", "args": [ "-y", "mcp-remote", "https://mcp.atlassian.com/v1/mcp", "--storage-dir", "/Users/username/.mcp-auth/site-sandbox" ] } } }
Each entry uses --storage-dir so that credentials for Site A do not overwrite Site B. When starting Claude Desktop, you will be prompted to authenticate twice in your browser. On the first consent screen, select Site 1 (e.g., Production); on the second, select Site 2 (e.g., Sandbox/Dev). Claude will automatically namespace the tool calls (e.g., jira-production__search vs. jira-sandbox__search).
--storage-dir
jira-production__search
jira-sandbox__search
If you manage instances where API tokens are permitted (or one site is external/sandbox), running local standalone MCP server processes (such as mcp-atlassian) gives you explicit per-server URL and credential bindings.
mcp-atlassian
Configuration (claude_desktop_config.json)
{ "mcpServers": { "jira-site-alpha": { "command": "uvx", "args": ["mcp-atlassian"], "env": { "JIRA_URL": "https://site-alpha.atlassian.net", "JIRA_USERNAME": "your-email@domain.com", "JIRA_API_TOKEN": "ATATT3x..." } }, "jira-site-beta": { "command": "uvx", "args": ["mcp-atlassian"], "env": { "JIRA_URL": "https://site-beta.atlassian.net", "JIRA_USERNAME": "your-email@domain.com", "JIRA_API_TOKEN": "ATATT3x..." } } } }
I hope this helps & resolves your issue. 🙂
Thanks, Anwesha
I agree with Anwesha's recommendation, you can use remote mcp, but the end points I'd use is v2 instead of v1: "https://mcp.atlassian.com/v2/mcp": https://developer.atlassian.com/cloud/rovo-mcp/guides/getting-started/
Hello @Buddhika Nanayakkara
For security, use Atlassian's official MCP endpoint with OAuth rather than storing API tokens.
There's also an earlier discussion where users successfully connected multiple sites using separate Claude custom connectors.
One correction: --storage-dir isn't documented for mcp-remote. The documented --resource option can separate OAuth sessions. Also, review MCP permissions in Atlassian Administration and follow least-privilege access. Are you using Claude Desktop, Claude.ai, or Claude Code?
Best, Arek 🤠
The official Atlassian Rovo MCP server (https://mcp.atlassian.com/v2/mcp) is designed to handle multiple Atlassian products and sites natively through a single authentication flow, provided those sites are within the same Atlassian Organization. Did you have a chance to explore this?
https://mcp.atlassian.com/v2/mcp
When you authenticate with the official Atlassian Rovo MCP server using OAuth 2.1, you are authorizing access to your Atlassian Organization.
getAccessibleAtlassianResources
Are you trying to connect sites from the same organization or from different ones?
Hi @Buddhika Nanayakkara,
On whether one OAuth login covers several sites: Atlassian's page on API token auth for the Rovo MCP server says OAuth tokens are "typically consented for a specific cloudId", while API tokens are "not bound to a specific cloudId". So with OAuth, separate connections per site (as suggested above) is the safe bet; a single connection across sites is what the token route gives you.
If you go the token route, the same page adds a few guardrails: an org admin has to enable it first, token requests are governed only by your IP allowlist (not domain allowlists), and you should tell the agent which cloudId to use before any write. A service account per site with only the scopes you need keeps each one easy to revoke.
Thank you for the detailed explanation. Let me have a look on this
Thank you. Let me check this
Thank you. I'm using Claude Desktop, and I do have Atlassian Administration permission. The issue is that Atlassian's official MCP endpoint supports only one Jira site. Isn't it?
Thank you. I'm trying to connect different sites from different organisations
Thanks everyone for your inputs
MCP itself isn't limited to one Jira site, but OAuth authorization is typically site-specific.
For different organizations, you can try separate named MCP connections in Claude Desktop, each authorized for the appropriate Jira site.
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