Setup Jira MCP Server

Setup Jira MCP Server

Install and configure the mcp-atlassian MCP server so Claude Code can interact with Jira directly.

Step 1 — Check Dependencies

Run the dependency check:

${CLAUDE_PLUGIN_ROOT}/scripts/check-deps.sh

If dependencies are missing, show the error output to the user and stop here. Do not proceed until all dependencies are satisfied.

Step 2 — Gather Credentials

If $ARGUMENTS provides all three values

Use them in order: <jira-url> <username> <api-token>.

Example: /jira-mcp-setup https://mycompany.atlassian.net [email protected] ATATT3x...

If arguments are missing or incomplete

Ask the user for each missing value:

1. Jira URL (required) — The Atlassian instance URL, e.g. https://mycompany.atlassian.net
2. Username / Email (required) — The email used to log in to Jira Cloud. The user can find it at https://id.atlassian.com/manage-profile
3. API Token (required) — The user must generate one at https://id.atlassian.com/manage-profile/security/api-tokens. Steps: click "Create API token", give it a name (e.g. "Claude Code"), and copy the token

Step 3 — Configure MCP

Run the setup script with the collected values:

${CLAUDE_PLUGIN_ROOT}/scripts/setup-mcp.sh "<jira-url>" "<username>" "<api-token>"

Step 4 — Protect Credentials

The .mcp.json file contains the API token in plain text. Ask the user if they want to add .mcp.json to .gitignore to prevent accidentally committing secrets.

• If .mcp.json is already listed in .gitignore, skip this step.
• If the user accepts, run:

${CLAUDE_PLUGIN_ROOT}/scripts/setup-mcp.sh --add-gitignore

• If the user declines, warn them that the file contains sensitive credentials and should not be pushed to a remote repository.

Step 5 — Present Result

After successful setup, tell the user:

1. The .mcp.json file has been created/updated in the project root
2. Whether .mcp.json was added to .gitignore
3. Restart Claude Code (or start a new conversation) for the Jira MCP server to activate
4. Once active, Claude will have direct access to Jira tools (search issues, create tickets, add comments, etc.)

Troubleshooting

If the user reports issues after setup:

• Verify the API token is valid at https://id.atlassian.com/manage-profile/security/api-tokens
• Ensure the Jira URL does not have a trailing slash
• Run uvx mcp-atlassian manually to test the server starts correctly