Best Practice to Connect Multiple Jira Instances to Claude

[Brian Griffin]

I have a technical question for the community that I haven’t been able to find much information on, either here in the Q&A or elsewhere online.

I currently have a paid company instance of Jira and a free personal instance of Jira, and I wanted to connect both to Claude Desktop. At first, I didn’t give much thought to how I should connect them. I knew I could use MCP and create a custom server if needed, but then I noticed Claude’s new built-in Connectors feature. It made connecting to popular apps like Jira and Google Calendar much easier.

I connected our paid company Jira account using the Connectors integration, and it went smoothly and worked perfectly. Later, when I tried to connect my personal Jira instance, I realized I couldn’t install multiple Jira connections within the Connectors settings. So, I decided to use MCP for the personal instance instead. It took a little longer to set up, but I eventually got it working.

At first, I assumed only one instance should be active at a time to avoid confusion when prompting Claude. I practiced switching between them for a few days, but curiosity got the better of me, and I asked Claude if it could see both instances at the same time. It turns out it could. It worked fine for a while, but my personal MCP connection started having issues with basic function calls like get_issues. Claude tried to fix the problem, and it worked at first, but things got worse afterward.

So here’s my question: What’s the best way to connect multiple Jira instances to Claude and configure them to work together without conflicts? If the best solution is to manually enable one connection at a time, that’s fine. I just want to make sure I can access the same tools across each instance without issue.