Configure Atlassian MCP server permissions

‌As an organization admin, you can control what data that the Atlassian MCP server can read, write, and search across your organization’s Atlassian apps and connected tools. You can turn permissions on or off from the table, or open Edit details to choose more specific permissions.

The Permissions in Atlassian Administration under Rovo and Rovo MCP server is now the primary way to control what the MCP server can access across your organization. Going forward, permissions configured here will take precedence over settings in Connected Apps or individual app permissions in Marketplace. To restrict or allow specific actions — such as preventing the MCP server from creating or editing content — use the Permissions tab.

For more details of the tools Atlassian MCP supports, see: Supported tools

What you can configure

Status in the table

Change permissions from the table

Step 1. Open Permissions

1. 移動 アトラシアンの管理。組織が複数ある場合は、対象の組織を選択します。

2. Select Rovo, then Rovo MCP server.

3. [権限] タブを選択します。

Step 2. Review Read, Write, and Search

1. Check the Status column for each permission.

2. Use the row checkboxes to turn a permission type on or off for all permissions where the UI allows it, or use Select all permissions in the header when you want to apply a bulk change.

Apply to future additions: When you allow an intent, that access is automatically granted to any new permissions that request the same permission. New permissions won’t require manual review by admins and will be available to users as soon as they’re added. Admins can change this behavior at any time in the Edit details dialog box.

If an update fails, try refreshing the page. If the problem continues, contact Atlassian Support.

Edit permissions per app

Use Edit details when you need different settings per app (for example Jira vs Confluence).

Step 1. Open Edit details

1. On the Permissions tab, find the permission type (for example, Read, Write, or Search).

2. Select the permission type to see a list of toolsets.

Step 2. Choose apps (permissions)

1. In the dialog box, review each app row and use the checkboxes to allow or block that permission for that app.

2. Optionally turn on Allow all, apply permissions to future additions automatically so new apps or permission sets inherit these settings.

This Apply to future additions control is the same idea as turning the permission on from the main table row checkbox: both mean new permission for that intent will receive access unless you change the setting again.

Step 3. Save and dismiss

1. Save your changes in the dialog box.

2. Read the confirmation banner and dismiss it with Understood when you're done.

What users see when a permission is blocked

When a permission is blocked, users connecting through an AI client (such as Claude, Cursor, or another MCP-compatible tool) will see the following error message:

Access denied: Your organization admin has not authorized the [permission name] permission.

For example: Access denied: Your organization admin has not authorized the write permission.

If users report this error, check the Permissions tab to confirm the relevant permission is set to Allowed. Changes take effect immediately — no restart or reconnection is required.

FAQ

This section lists the exact error messages that users or admins may encounter as a result of this change.

End-user facing errors (shown in AI client e.g. Claude, Cursor)

Q: A user reports they can't use a tool and sees an error. What does it say?

There are three possible error messages depending on the scenario:

Resolution for each:

• "Access denied: Your organization admin has not authorized..." — The admin needs to go to Permissions in Atlassian Administration (see previous steps on this page) and set the relevant permission to Allowed. Changes take effect immediately.

• "We are having trouble verifying your organization permissions..." — Confirm the user's Atlassian account is associated with the correct organization. If the issue persists, escalate to engineering.

• "We are having trouble completing this action..." — Ask the user to retry. If persistent, contact Atlassian Support.

Admin-facing errors (shown in Atlassian Administration)

These are the exact error messages that you, as an organization admin, may see in Atlassian Administration when managing the Atlassian MCP permissions.

Permissions tab — loading error

Shown as a full-page empty state when the Permissions tab fails to load toolset data (e.g. network or API error):

Permissions tab — toggle / save errors

Shown as a flag (toast notification) when an admin tries to enable or block a permission row (Read, Write, Search) and the mutation fails, or when saving changes in the Edit details dialog box fails:

Resolution: Ask the admin to refresh the page and try again. If the problem persists, contact Atlassian Support.

Other policy-related errors (not specific to toolset enforcement)

These may be seen by users in other scenarios and should not be confused with toolset permission errors: