Atlassian MCP in Claude Code: Jira and Confluence, properly wired

The command

claude mcp add --transport http atlassian https://mcp.atlassian.com/v1/mcp/authv2

# then, inside a session, complete the browser sign-in
/mcp

claude mcp remove atlassian
claude mcp logout atlassian     # drop the old OAuth grant
claude mcp add --transport http atlassian https://mcp.atlassian.com/v1/mcp/authv2
claude mcp list

OAuth or API token

Two authentication paths, and they are not interchangeable. The product coverage genuinely differs, which is the single most useful thing on this page.

• OAuth 2.1 is the default and the right choice for a person at a laptop. Browser sign-in, no secret in any file, and every action runs with the permissions your Atlassian account already has.
• API tokens are for headless and service use, and for Jira Service Management or Bitbucket, which OAuth does not cover. They need an admin to enable token access in Atlassian Administration first, and a scoped personal token.

claude mcp list                 # ! Needs authentication until you sign in
claude mcp login atlassian      # run the OAuth flow from the shell
claude mcp login atlassian --no-browser   # over SSH: prints the URL instead
claude mcp get atlassian

That --no-browser variant matters more than it sounds. Plenty of people run Claude Code on a remote box over SSH, where the OAuth flow cannot open a browser. It prints the authorisation URL, you open it locally, then paste the full redirect URL back. Connect with ssh -t so the paste prompt has a terminal.

Rate limits and plans

The hourly ceiling is a real constraint for one specific pattern: asking an agent to sweep a board. "Summarise every open ticket in the sprint" is dozens of calls, and on a Free plan a couple of those in an afternoon is the budget gone. Sprint sweeps belong in a search query, not a loop.

What it is actually good for

The value is not that Claude can read a ticket. It is that the ticket, the branch, the diff, and the pull request stop being four windows you are copying between.

Read ENG-4521, then plan the change against this repo before writing anything.

Implement it. Use the acceptance criteria from the ticket as the test cases.

Open a PR, link it to ENG-4521, and move the ticket to In Review with a comment
summarising what changed and what still needs a human decision.

Confluence is the half people forget

The same server reaches Confluence, and for most teams that is where the answer to "why is it built this way" actually lives. An agent that can search the space before it starts writing produces markedly better plans, because the constraint it would otherwise rediscover by breaking something is written down.

Before you plan this, search Confluence in the ENG space for anything about
rate limiting or idempotency keys, and quote what you find. If there is a
decision record that contradicts the ticket, say so instead of proceeding.

Write access to Confluence is a different risk calculation from write access to Jira. A wrong Jira transition is a two-click undo. A page rewritten in place has a version history that nobody reads. Keep Confluence at read unless the workflow is explicitly about drafting documentation.

Asking for the right thing

The difference between this server being useful and being a rate-limit generator is almost entirely in how you phrase the request. Jira is a query engine with a query language, and an agent handed a vague instruction will fall back to fetching things one at a time.

Scoping which tools it may use

Atlassian tools are addressable like any other MCP tool, as mcp__<server>__<tool> using the name you gave the server. That lets you auto-approve reads and keep a prompt in front of anything that changes a ticket.

{
  "permissions": {
    "allow": [
      "mcp__atlassian__get*",
      "mcp__atlassian__search*"
    ],
    "ask": [
      "mcp__atlassian"
    ]
  }
}

When it will not connect

claude mcp remove atlassian
claude mcp logout atlassian
claude mcp add --transport http atlassian https://mcp.atlassian.com/v1/mcp/authv2
claude mcp login atlassian
claude mcp list

Questions people ask

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