Configure tools for an external MCP server
An MCP server is a service that implements the Model Context Protocol (MCP) to expose tools and data to AI agents in a standardized way. It acts as a bridge between AI clients (like ChatGPT, Claude, or Rovo) and external systems so the AI can securely discover and call those systems’ capabilities (for example, via APIs) using natural language.
Before you begin
Make sure:
You’re an organization admin or have equivalent permissions to manage MCP servers in Atlassian Administration.
You’ve confirmed with relevant teams (for example, security, platform, or app owners) that it’s safe to configure this MCP server, and that impacted AI use cases have been reviewed.
Configure external MCP server settings
After adding an external MCP server from Atlassian Administration, you can configure which tools can be integrated into Rovo and other AI features by users in your organization.
To configure the settings of an external MCP server:
Go to Atlassian Administration. Select your organization if you have more than one.
From the sidebar menu, expand Apps.
Expand Sites then select the site where the MCP server is located.
Select Connected apps.
From the list of connected apps, locate the MCP server.
Under the Actions column, select View app details.
Select the Tools selection tab.
Find one or more MCP tools you want to deactivate and deselect the checkbox for the tools.
Once deactivated, the tools will no longer be available to users. You can return to the same screen at any time to reactivate tools if needed.
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