How to integrate Atlassian MCP with Atomic Agent

Connect Atomic Agent to Atlassian MCP. Create a jira issue for outage, list open jira issues assigned to me, and more using natural language, with authentication handled for you.

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Atlassian Rovo MCP connects agents to Jira, Jira Service Management, Confluence, Bitbucket, Compass, and Teamwork Graph workflows. It lets teams surface and act on Atlassian data while respecting existing user permissions.

40 Tools

Introduction

Atomic Agent is an open-source AI agent that runs on your machine and supports local models through llama.cpp. Connect it to 1,500+ apps through Composio, including Atlassian.

This guide uses Atomic Agent's built-in Composio integration. You need Atomic Agent v0.5.6 or later, your own Composio API key, and a Atlassian account. See the Atomic Agent documentation for installation instructions.

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How Atomic Agent connects to Atlassian

Atomic Agent connects to Composio's Tool Router over Streamable HTTP MCP. It discovers the tools needed for your request, and Composio handles account authentication.

Execution and account-connection tools follow Atomic Agent's configured approval policy. Review any approval prompt before allowing an action on your connected account.

Connect Atlassian to Atomic Agent

  1. Sign up or sign in to the Composio dashboard. Copy your API key.
  2. In Atomic Agent, open the Integrations tab and select Composio. Select API key, press e, paste the key, and press Enter. The tools become available immediately, without a restart.
  3. Ask Atomic Agent to do something in Atlassian. It searches Composio for the right tool.
  4. On first use, open the sign-in link returned in the chat. Connect your Atlassian account, then return to Atomic Agent to continue.

Headless setup

Add the following line to ~/.atomic-agent/.env, replacing YOUR_COMPOSIO_API_KEY with your key. Start Atomic Agent after saving the file.

bash
COMPOSIO_API_KEY=YOUR_COMPOSIO_API_KEY

What is the Atlassian MCP server, and what's possible with it?

The Atlassian MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Atlassian account. It provides structured and secure access so your agent can perform Atlassian operations on your behalf.

Use Atlassian from Atomic Agent

With your account connected, ask Atomic Agent to work with Atlassian in natural language. You can connect more apps through the same Composio integration as you need them.

Visit the Atomic Agent website or inspect the Atomic Agent source code.

Troubleshooting

Why is my API key rejected?

Copy the key directly from the Composio dashboard. Atomic Agent requires ASCII characters because it sends the key in an HTTP header. Remove any extra characters introduced when copying.

Why are Composio tools unavailable after saving a key?

Check that you use Atomic Agent v0.5.6 or later and that Composio is enabled in your configuration. A "composio": { "enabled": false } setting disables the integration while keeping the saved key on disk.

Does Composio have a free plan?

The Hobby plan includes 100,000 tool calls per month. Composio-managed OAuth apps have a lower included allowance. See Composio pricing for the current limits that apply to your connection.

TOOLS

Supported Tools

Every Atlassian MCP action and event your agent gets out of the box.

Addcommenttojiraissue

Add or update a comment on a Jira issue

Addteamworkgraphcontext

Adds a relationship between two entities in the Teamwork Graph (e.

Addworklogtojiraissue

Add or update a worklog on a Jira issue.

Atlassianuserinfo

Get current user info

Createcompasscomponent

Create a new Compass component

Createcompasscomponentrelationship

Create a relationship between Compass components

Createcompasscustomfielddefinition

Create a custom field definition in Compass

Createconfluencefootercomment

Create a footer comment on a page or blog post

Createconfluenceinlinecomment

Create an inline comment on specific text in a page or blog post.

Createconfluencepage

Create a Confluence page or blog post

Createissuelink

Create a link between two Jira issues.

Createjiraissue

Create a Jira issue.

Editjiraissue

Update issue.

Fetch

Get details of a Jira issue or Confluence page by ARI (Atlassian Resource Identifier), if the id is not an ARI, then use a different tool to fetch the content

Getaccessibleatlassianresources

Get cloudId to make tool calls.

Getcompasscomponent

Get a Compass component by ID

Getcompasscomponents

Get a list of Compass components

Getcompasscustomfielddefinitions

Get a list of Compass custom field definitions

Getconfluencecommentchildren

Get reply(child) comments for a comment

Getconfluencepage

Get a Confluence page or blog post by ID, including body content.

Getconfluencepagedescendants

Get child pages of specified page

Getconfluencepagefootercomments

Get footer comments for a page or blog post

Getconfluencepageinlinecomments

Get inline comments for a page or blog post

Getconfluencespaces

Get spaces

Getissuelinktypes

Get available Jira issue link types (e.

Getjiraissue

Get issue details

Getjiraissueremoteissuelinks

Get remote links

Getjiraissuetypemetawithfields

Get field metadata

Getjiraprojectissuetypesmetadata

Get issue types

Getpagesinconfluencespace

Get pages or blog posts in a space

Getteamworkgraphcontext

Retrieves connected context from Teamwork Graph for any Atlassian entity.

Getteamworkgraphobject

Fetches the entire available data for one or more objects (Atlassian or third-party) using their ARIs or URLs.

Gettransitionsforjiraissue

Get transitions

Getvisiblejiraprojects

Get projects

Lookupjiraaccountid

Lookup user IDs

Search

Search Jira and Confluence using Rovo Search, ALWAYS use this tool to search for Jira and Confluence content unless the word CQL or JQL is used in the context

Searchconfluenceusingcql

Search Confluence content (pages, blog posts, comments, attachments) using CQL (Confluence Query Language).

Searchjiraissuesusingjql

Search issues with JQL, total counts only when explicitly requested.

Transitionjiraissue

Transition issue status

Updateconfluencepage

Update a Confluence page or blog post

FAQ

Frequently asked questions

With a standalone Atlassian MCP server, the agents and LLMs can only access a fixed set of Atlassian tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Atlassian and many other apps based on the task at hand, all through a single MCP endpoint.

Yes, you can. Atomic Agent fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Atlassian tools.

Yes, absolutely. You can configure which Atlassian scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Atlassian data and credentials are handled as safely as possible.

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