# How to integrate Atlassian MCP with Atomic Agent

```json
{
  "title": "How to integrate Atlassian MCP with Atomic Agent",
  "toolkit": "Atlassian MCP",
  "toolkit_slug": "atlassian_mcp",
  "framework": "Atomic Agent",
  "framework_slug": "atomic-agent",
  "url": "https://composio.dev/toolkits/atlassian_mcp/framework/atomic-agent",
  "markdown_url": "https://composio.dev/toolkits/atlassian_mcp/framework/atomic-agent.md",
  "updated_at": "2026-09-01T05:32:42.301Z"
}
```

## 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](https://atomicagent.io/docs/?cta_placement=atomic-agent-docs) for installation instructions.

## Also integrate Atlassian MCP with

- [ChatGPT](https://composio.dev/toolkits/atlassian_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/atlassian_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/atlassian_mcp/framework/hermes-agent)

## TL;DR

### 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 MCP to Atomic Agent

### Connect Atlassian to Atomic Agent
- Sign up or sign in to the [Composio dashboard](https://dashboard.composio.dev/?cta_placement=atomic-agent-api-key). Copy your API key.
- 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.
- Ask Atomic Agent to do something in Atlassian. It searches Composio for the right tool.
- 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.

## Supported Tools

| Tool slug | Name | Description |
|---|---|---|
| `ATLASSIAN_MCP_ADD_COMMENT_TO_JIRA_ISSUE` | Addcommenttojiraissue | Add or update a comment on a Jira issue |
| `ATLASSIAN_MCP_ADD_TEAMWORK_GRAPH_CONTEXT` | Addteamworkgraphcontext | 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 project or goal). |
| `ATLASSIAN_MCP_ADD_WORKLOG_TO_JIRA_ISSUE` | Addworklogtojiraissue | Add or update a worklog on a Jira issue. When worklogId is provided, updates that worklog; |
| `ATLASSIAN_MCP_ATLASSIAN_USER_INFO` | Atlassianuserinfo | Get current user info |
| `ATLASSIAN_MCP_CREATE_COMPASS_COMPONENT` | Createcompasscomponent | Create a new Compass component |
| `ATLASSIAN_MCP_CREATE_COMPASS_COMPONENT_RELATIONSHIP` | Createcompasscomponentrelationship | Create a relationship between Compass components |
| `ATLASSIAN_MCP_CREATE_COMPASS_CUSTOM_FIELD_DEFINITION` | Createcompasscustomfielddefinition | Create a custom field definition in Compass |
| `ATLASSIAN_MCP_CREATE_CONFLUENCE_FOOTER_COMMENT` | Createconfluencefootercomment | Create a footer comment on a page or blog post |
| `ATLASSIAN_MCP_CREATE_CONFLUENCE_INLINE_COMMENT` | Createconfluenceinlinecomment | Create an inline comment on specific text in a page or blog post. For top-level comments, provide pageId and inlineCommentProperties (text selection + match counts). For replies, provide parentCommentId only (no pageId or inlineCommentProperties). You must first fetch the page content (e.g. using getConfluencePage) to find the exact text and count how many times it appears. Incorrect or missing inlineCommentProperties can result in a 400 error from the Confluence API. |
| `ATLASSIAN_MCP_CREATE_CONFLUENCE_PAGE` | Createconfluencepage | Create a Confluence page or blog post |
| `ATLASSIAN_MCP_CREATE_ISSUE_LINK` | Createissuelink | Create a link between two Jira issues. For directional link types (e.g. Blocks): inwardIssue = issue that blocks, outwardIssue = issue that is blocked (e.g. "A is blocked by B" → inwardIssue: B, outwardIssue: A). Use getIssueLinkTypes if link type is unknown. |
| `ATLASSIAN_MCP_CREATE_JIRA_ISSUE` | Createjiraissue | Create a Jira issue. Use additional_fields to set any Jira field that does not have its own parameter (e.g. custom fields, priority, components). |
| `ATLASSIAN_MCP_EDIT_JIRA_ISSUE` | Editjiraissue | Update issue. After updating, returns the issue using the same default read fields as getJiraIssue (summary, description, status, issuetype, priority, labels, components, assignee, reporter, created, updated, resolution, project). Use getJiraIssue with fields ["*all"] or a custom list if you need more. |
| `ATLASSIAN_MCP_FETCH` | 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 |
| `ATLASSIAN_MCP_GET_ACCESSIBLE_ATLASSIAN_RESOURCES` | Getaccessibleatlassianresources | Get cloudId to make tool calls. When a link is provided (e.g. https://site.atlassian.net/*), try passing the site hostname (e.g. site.atlassian.net) as cloudId to other tools first; if that fails, use this tool to list accessible resources. |
| `ATLASSIAN_MCP_GET_COMPASS_COMPONENT` | Getcompasscomponent | Get a Compass component by ID |
| `ATLASSIAN_MCP_GET_COMPASS_COMPONENTS` | Getcompasscomponents | Get a list of Compass components |
| `ATLASSIAN_MCP_GET_COMPASS_CUSTOM_FIELD_DEFINITIONS` | Getcompasscustomfielddefinitions | Get a list of Compass custom field definitions |
| `ATLASSIAN_MCP_GET_CONFLUENCE_COMMENT_CHILDREN` | Getconfluencecommentchildren | Get reply(child) comments for a comment |
| `ATLASSIAN_MCP_GET_CONFLUENCE_PAGE` | Getconfluencepage | Get a Confluence page or blog post by ID, including body content. |
| `ATLASSIAN_MCP_GET_CONFLUENCE_PAGE_DESCENDANTS` | Getconfluencepagedescendants | Get child pages of specified page |
| `ATLASSIAN_MCP_GET_CONFLUENCE_PAGE_FOOTER_COMMENTS` | Getconfluencepagefootercomments | Get footer comments for a page or blog post |
| `ATLASSIAN_MCP_GET_CONFLUENCE_PAGE_INLINE_COMMENTS` | Getconfluencepageinlinecomments | Get inline comments for a page or blog post |
| `ATLASSIAN_MCP_GET_CONFLUENCE_SPACES` | Getconfluencespaces | Get spaces |
| `ATLASSIAN_MCP_GET_ISSUE_LINK_TYPES` | Getissuelinktypes | Get available Jira issue link types (e.g. Blocks, Duplicate, Clones, Relates). For createIssueLink: inwardIssue = blocker, outwardIssue = blocked (e.g. "A is blocked by B" → inwardIssue: B, outwardIssue: A). |
| `ATLASSIAN_MCP_GET_JIRA_ISSUE` | Getjiraissue | Get issue details |
| `ATLASSIAN_MCP_GET_JIRA_ISSUE_REMOTE_ISSUE_LINKS` | Getjiraissueremoteissuelinks | Get remote links |
| `ATLASSIAN_MCP_GET_JIRA_ISSUE_TYPE_META_WITH_FIELDS` | Getjiraissuetypemetawithfields | Get field metadata |
| `ATLASSIAN_MCP_GET_JIRA_PROJECT_ISSUE_TYPES_METADATA` | Getjiraprojectissuetypesmetadata | Get issue types |
| `ATLASSIAN_MCP_GET_PAGES_IN_CONFLUENCE_SPACE` | Getpagesinconfluencespace | Get pages or blog posts in a space |
| `ATLASSIAN_MCP_GET_TEAMWORK_GRAPH_CONTEXT` | Getteamworkgraphcontext | Retrieves connected context from Teamwork Graph for any Atlassian entity. Returns all relationships and linked objects within one traversal – including cross-product and third-party connections. Use when the answer requires connections between entities, not just a single entity's fields. Supported entry points: Jira: issues, projects, sprints, versions, comments Confluence: pages, blogposts, whiteboards, databases, spaces Goals, Projects, Focus Areas, Tags and updates People: users, teams, organisations DevOps: PRs, repos, deployments, services, builds, designs Loom: videos, meetings Compass: components Assets: objects Incidents, conversations, calendar events, external documents After calling this tool, call getTeamworkGraphObject on returned ARIs to get full content. |
| `ATLASSIAN_MCP_GET_TEAMWORK_GRAPH_OBJECT` | Getteamworkgraphobject | Fetches the entire available data for one or more objects (Atlassian or third-party) using their ARIs or URLs. Use for the objects gathered from getTeamworkGraphContext tool. |
| `ATLASSIAN_MCP_GET_TRANSITIONS_FOR_JIRA_ISSUE` | Gettransitionsforjiraissue | Get transitions |
| `ATLASSIAN_MCP_GET_VISIBLE_JIRA_PROJECTS` | Getvisiblejiraprojects | Get projects |
| `ATLASSIAN_MCP_LOOKUP_JIRA_ACCOUNT_ID` | Lookupjiraaccountid | Lookup user IDs |
| `ATLASSIAN_MCP_SEARCH` | 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 |
| `ATLASSIAN_MCP_SEARCH_CONFLUENCE_USING_CQL` | Searchconfluenceusingcql | Search Confluence content (pages, blog posts, comments, attachments) using CQL (Confluence Query Language). CQL is specific to Confluence and is not interchangeable with JQL. |
| `ATLASSIAN_MCP_SEARCH_JIRA_ISSUES_USING_JQL` | Searchjiraissuesusingjql | Search issues with JQL, total counts only when explicitly requested. |
| `ATLASSIAN_MCP_TRANSITION_JIRA_ISSUE` | Transitionjiraissue | Transition issue status |
| `ATLASSIAN_MCP_UPDATE_CONFLUENCE_PAGE` | Updateconfluencepage | Update a Confluence page or blog post |

## Supported Triggers

None listed.

## 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](/pricing) for the current limits that apply to your connection.

## Complete Code

None listed.

## Conclusion

### 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](https://atomicagent.io/?cta_placement=atomic-agent-site) or inspect the [Atomic Agent source code](https://github.com/AtomicBot-ai/atomic-agent?cta_placement=atomic-agent-repo).

## How to build Atlassian MCP Agent with another framework

- [ChatGPT](https://composio.dev/toolkits/atlassian_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/atlassian_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/atlassian_mcp/framework/hermes-agent)

## Related Toolkits

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- [Breathe HR](https://composio.dev/toolkits/breathehr) - Breathe HR is cloud-based HR software for SMEs to manage employee data, absences, and performance. It simplifies HR admin, making it easy to keep employee records accurate and up to date.

## Frequently Asked Questions

### What are the differences in Tool Router MCP and Atlassian MCP?

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.

### Can I use Tool Router MCP with Atomic Agent?

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.

### Can I manage the permissions and scopes for Atlassian while using Tool Router?

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.

### How safe is my data with Composio Tool Router?

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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