Atlassian MCP / App in amberAI for Administrators

Guide: Connecting the Atlassian MCP Server with amber (Administrator Guide)

What is the Atlassian Rovo MCP Server?

The Atlassian Rovo MCP Server (Model Context Protocol) is an integration layer that allows external AI tools like amberAI to securely access Jira, Confluence, and Compass. Users can then perform actions directly from an amberAI conversation – e.g., create issues, manage sprints, or create Confluence pages.

💡 Important: The Atlassian MCP Server supports Atlassian Cloud only – on-premise instances are not supported.

Prerequisites

Area Prerequisite

Atlassian

Atlassian Cloud instance (Jira, Confluence, and/or Compass)

Atlassian

Org admin rights in Atlassian Administration

amber

Active amber account with administrator access

amber

amberAI is enabled for the organization

Part 1: Configuration on the Atlassian Side

Step 1: Choose Authentication Method

The Atlassian Rovo MCP Server supports two authentication methods:

Method Description Recommendation

OAuth 2.1

Users connect via an OAuth consent screen. Access is limited to the existing permissions of the respective user.

✅ Recommended (Default)

API Token

Enables service-style connections without user-based OAuth consent. Useful for non-interactive tools.

Advanced / Service Use Cases

Step 2: Configure Domain Settings

In Atlassian Administration under the Atlassian Rovo MCP Server Settings:

  1. Review Atlassian-supported domains: Atlassian provides a default list of supported AI partner domains (e.g., Anthropic, OpenAI). These domains are allowed by default.

  2. Authorize custom domains: If amber is not included in the default list, add your amber domain as a trusted domain. e.g. https://customerName.ambersearch.de/** .

    Add the two stars at the end to cover every subsite. (How to format URLs).

  3. Manage the entire domain list: Note that you can only allow or block the Atlassian-supported domains as an entire list – individual domains cannot be blocked separately.

Step 3: Consider IP Allowlisting (if active)

If your organization uses IP allowlisting, these policies also apply to MCP server access:

  • IP allowlists are managed in Atlassian Administration (not in the MCP server settings).

  • For a tool call to succeed, the request must originate from an allowed IP address.

  • Caution: Some AI tools use their own outgoing IP addresses. Even if the user is connected via a corporate VPN, calls may be blocked if the tool's IP ranges are not included in the allowlist.

⚠️ The OAuth 2.1 consent screen may still appear for users connecting from blocked IPs – however, the actual tool calls will fail.

Step 4: Enable API Token Authentication (optional)

If you want to use the API token method:

  • Enable this in the Atlassian Rovo MCP Server Settings at the organization level.

  • This method is particularly suited for service-style or non-interactive integrations.

Part 2: Configuration on the amber Side

Step 1: Set Up MCP Server in the amber Admin Dashboard

As an administrator, set up the Atlassian MCP Server in amber so that it becomes available to users in the app overview. The Help Center user documentation assumes that "the Atlassian MCP Server has been set up by your administrator."

Step 2: Enter Configuration Data

Enter the necessary connection data in the amber Admin Dashboard:

  • MCP Server URL: The Atlassian Rovo MCP Server endpoint URL

    https://mcp.atlassian.com/v1/mcp (See official documentation)

  • Authentication method: OAuth 2.1 or API Token (depending on the choice in Step 1 on the Atlassian side)

Part 3: User Connection (after Admin Setup)

After you as an admin have completed the setup, users must establish the connection individually:

  1. Open user settings → Click on your own name in the bottom left corner of amber

  2. Navigate to: User Settings → Connectors → Apps

  3. Select Atlassian MCP Server – the server provided by the admin appears in the app overview

  4. Establish connection – follow the authentication flow (OAuth or API Token)

  5. Reload the page – the Atlassian integration is now active

🔒 Each user must connect to the MCP server individually. amber always respects the personal access permissions of the respective user.

Rate Limits

Note the Atlassian-side rate limits depending on the plan:

Atlassian Plan Calls per Hour

Free

500

Standard

1,000

Premium / Enterprise

1,000 (+ 20 per user, max. 10,000)

Checklist for Admins

  • Atlassian Cloud instance available

  • Authentication method chosen (OAuth 2.1 recommended)

  • amber domain authorized in the Atlassian MCP Server domain settings

  • IP allowlisting reviewed and amber IP ranges added if necessary

  • For API Token:Setting enabled at the organization level in Atlassian

  • MCP Server set up in the amber Admin Dashboard

  • Users informed about the individual connection process

Security Notes

  • MCP clients can perform actions in Jira, Confluence, and Compass with the existing permissions of the user.

  • Apply the principle of least privilege and review high-impact changes before confirming.

  • Monitor audit logs for unusual activity.

  • The Atlassian MCP Server does not store or cache any Jira or Confluence content – it acts as a secure proxy.