Atlassian MCP

The Atlassian MCP (Atlassian Rovo MCP Server) is a cloud-based bridge between your Atlassian Cloud site and compatible AI tools. Once configured through Cequence AI Gateway, it enables those tools to interact with Jira, Compass, and Confluence data in real time using secure OAuth 2.1 authorization, with all actions respecting your existing access controls.

1. Overview

The Atlassian MCP is a remote, vendor-hosted MCP server provided by Atlassian. You do not run the server yourself; you connect to it from Cequence AI Gateway using the server URL and OAuth.

• Server URL: https://mcp.atlassian.com/v1/mcp
• Transport: HTTP (Streamable HTTP). The /sse endpoint is also supported, but /mcp is recommended.
• Hosted by: Atlassian

It is designed for developers, content creators, and project teams who use IDEs or AI platforms and want to work with Atlassian data without constantly switching context.

2. Supported authentication types

Type	Supported	Notes
OAuth 2.1	Yes	Required. Secure browser-based OAuth 2.1 (3LO) flow; all traffic encrypted via HTTPS (TLS 1.2+). Access respects Jira, Compass, and Confluence permissions.
API key	No	Not used for the remote MCP server.
Other	No	—

When you add Atlassian MCP in Cequence AI Gateway, authentication is handled via OAuth 2.1. You sign in with your Atlassian Cloud account and grant access during the gateway flow. OAuth tokens are scoped and session-based.

For more detail, see Authentication and authorization in the official docs.

3. What can you do with this MCP server

With the Atlassian MCP server, you can:

• Summarize and search Jira, Compass, and Confluence content without switching tools.
• Create and update issues or pages based on natural language commands.
• Automate repetitive work, such as generating tickets from meeting notes or specs.

Capabilities vary by your permission level and the client you use. For a full list of tools, see Supported tools in the official documentation.

4. Prerequisites

Before adding Atlassian MCP in Cequence AI Gateway, ensure you have:

• Access to Cequence AI Gateway (e.g. beta.aigateway.cequence.ai)
• An Atlassian Cloud site with Jira, Compass, and/or Confluence
• A modern browser to complete the OAuth 2.1 authorization flow
• For OAuth authentication: an auth app with client credentials (client ID and client secret) in your vendor account, unless the server supports Dynamic Client Registration (DCR).
• Permission to connect: the first user to complete the 3LO consent flow for your site must have access to the Atlassian apps requested by the MCP (e.g. Jira and/or Confluence) so the MCP app is registered with the correct permissions. After that, users with access to only one app can also connect.

If your organization uses IP allowlisting for Atlassian Cloud, requests through the Atlassian MCP Server must come from an allowed IP address.

5. Example workflows

Once connected, you can run workflows like these from your client.

Jira

• Search: “Find all open bugs in Project Alpha.”
• Create/update: “Create a story titled ‘Redesign onboarding’.”
• Bulk create: “Make five Jira issues from these notes.”

Confluence

• Summarize: “Summarize the Q2 planning page.”
• Create: “Create a page titled ‘Team Goals Q3’.”
• Navigate: “What spaces do I have access to?”

Compass

• Create: “Create a service component based on the current repository.”
• Bulk create: “Import components and custom fields from this CSV/JSON.”
• Query: “What depends on the api-gateway service?”

Combined

• Link content: “Link these three Jira tickets to the ‘Release Plan’ page.”
• Find documentation: “Fetch the Confluence documentation page linked to this Compass component.”

6. Connecting MCP server from Cequence AI Gateway

1. Log in to Cequence AI Gateway.
2. Choose your tenant.
3. Go to App catalogue.
4. Filter by Remote MCP server.
5. Search for Atlassian MCP and then select it.
6. Click Create MCP server.
7. Choose auth method. If OAuth, you need an auth app with client credentials in your vendor account (see Prerequisites).
8. Complete the setup as prompted, select tools, and deploy.

Use the generated MCP server URL in your client as described in the Client Configuration docs. For detailed UI steps and screenshots, see Create a third-party MCP Server.

7. Additional information specific to Atlassian MCP

• Installation: The Atlassian MCP Server is not installed via the Atlassian Marketplace or Manage apps. It is provisioned automatically the first time a user completes the OAuth 2.1 (3LO) consent flow (“just-in-time” installation). A site or org admin may need to complete this flow first.
• Admin controls: Site and organization admins can manage, review, or revoke the MCP app’s access from Manage your organization's Marketplace and third-party apps. The app appears in your site’s Connected apps list after the first successful 3LO consent. Domain and IP controls are available under Rovo MCP server settings in Atlassian Administration.
• Audit logging: Key actions performed via the Atlassian MCP Server are logged in your organization’s audit log.
• Timeout: The remote server uses a 30-second timeout for requests.
• Official documentation: For setup, supported tools, client setup, and troubleshooting, see the Atlassian Rovo MCP Server documentation. For Atlassian Cloud APIs, see developer.atlassian.com/cloud.

Troubleshooting

• “Your site admin must authorize this app”: A site admin must complete the 3LO consent flow before others can use the MCP app. See “Your site admin must authorize this app” error for details.
• “You don't have permission to connect from this IP address”: Usually indicates IP allowlisting; your current IP may not be allowed. Ask your admin to review the IP allowlist and add the relevant network or VPN ranges if appropriate.
• App not appearing in Connected apps: Confirm the user is on the correct Atlassian account and site, and that the app is requesting the correct scopes (e.g. Jira, Confluence). Check Manage your organization's Marketplace and third-party apps or contact Atlassian Support.