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Connect Atlassian to Claude Code

Give Claude Code governed access to Atlassian’s 96 tools through Runlayer, with identity, policy, scanning, and audit on every call.

Book a demo Claude Code setup guide

Set up

Add Atlassian to Claude Code in four steps

Admins approve the server once. Everyone in Claude Code then gets it through the same governed connection.

  1. 1

    Approve Atlassian in Runlayer

    Add Atlassian from the catalog and choose who can use it and which of its tools are allowed.

  2. 2

    Connect Claude Code to Runlayer

    Runlayer’s CLI installs the Runlayer Plugin natively in Claude Code, and an Anthropic org install also reaches Claude Code. With direct tool listing turned on for your deployment, Atlassian’s 96 tools show up in Claude Code’s own tool list (supported Claude Code versions).

    Claude Code setup guide
  3. 3

    Sign in to Atlassian

    Sign in the way Atlassian requires. Runlayer holds the credentials so they stay out of the client’s configuration.

  4. 4

    Use Atlassian from Claude Code

    Atlassian’s approved tools appear in Claude Code. Every call is checked against policy and recorded.

Tools

96 Atlassian tools in Claude Code

Runlayer policy decides which of these Claude Code users can call. 12 read data only and 1 can change or delete data.

  • Add comment to Jira issue

    Add or update a comment on a Jira issue

  • Add Confluence content permissions

    Adds one or more content-level permission grants to a single Confluence content entity.

  • Add Confluence reaction

    Add emoji reaction to Confluence content

  • Add connections to goals

    Add one type of connection to one or more Atlassian Goals.

  • Add connections to projects

    Add one type of connection to one or more Atlassian Projects.

  • Add Teamwork Graph context

    Adds a relationship between two entities in the Teamwork Graph (e.g. linking two Jira work items, marking one as blocking another, attaching a remote link, or connecting a Jira work item to an Atlas…

  • Add labels to Confluence content

    Add labels to any Confluence content (page, blogpost, attachment, custom content)

  • Add or edit Jira issue comment

    Add a comment to a Jira issue, or edit an existing one: omit commentId to add, or pass one from listJiraIssueComments to edit.

See all 96 Atlassian tools

Control

What Runlayer can see and stop in Claude Code

Some controls apply to every client at the gateway. Others depend on what Claude Code exposes to Runlayer.

  • Gateway policy (available)

    Every Atlassian call from Claude Code passes through Runlayer, where your policies can allow, alert, mask, or block it.

  • Audit trail (available)

    Each call is recorded with the user, Claude Code as the client, the tool, and the policy and scanner decisions.

  • Client hooks (available)

    Capture supported prompts, reasoning, local and MCP tool calls, responses, and scanner decisions in real time.

  • Anthropic inference hooks (available)

    With Claude Enterprise, Anthropic sends each governed Claude Code prompt to Runlayer before inference, with nothing installed on devices (Anthropic beta).

  • OTLP telemetry (available)

    Claude Code can export OpenTelemetry logs to Runlayer for observe-only session reconstruction.

  • Stop a call before it runs (available)

    Runlayer can deny a tool call before Claude Code runs it.

  • Block output after it runs (available)

    Runlayer can block a tool’s output before Claude Code’s model sees it.

  • Redact output in place (available)

    Runlayer can mask sensitive parts of a tool’s output in Claude Code and pass the rest through.

In Claude Code

  • When a tool fails, Runlayer records the error but cannot hide it.

Frequently asked questions

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