Atlassian MCP API Authentication

How to authenticate Atlassian MCP API requests: one Bearer API key plus a connectionId. MindCloud stores your credentials — no auth headers to build.

Every Atlassian MCP API request through MindCloud needs two things: a MindCloud API Key and a connectionId for your Atlassian MCP account. This page covers both, plus exactly how to send them, so you do not need to visit any other page to get authenticated.

Steps to authenticate

Create a MindCloud account at app.mindcloud.co if you do not already have one.
Generate a MindCloud API Key in API Keys. This is the Bearer token you send on every request. Keep it on your server.
Create a Atlassian MCP connection in Connections. Atlassian MCP uses a username and password. You enter them when you create the connection — MindCloud stores them securely so your requests never carry raw credentials.
Copy the connection’s connectionId — you will send it on every request alongside your MindCloud API Key.

How requests are authenticated

Authentication has two layers. Your MindCloud API Key authenticates the request to MindCloud, sent as a Bearer token in the Authorization header. The connectionId selects the connected Atlassian MCP account that should run the action. MindCloud stores and refreshes the Atlassian MCP credentials behind that connection, so you never send provider tokens with your requests.

Pass connectionId in the query string for GET and DELETE actions, and in the JSON body for POST, PUT, and PATCH actions.

For example, calling Initialize Session with an Atlassian MCP connection looks like this:

curl --request POST \
  --url "https://connect.mindcloud.co/v2/universal/apps/atlassianMCP/actions/initialize-session/run" \
  --header "Authorization: Bearer $MINDCLOUD_API_KEY" \
  --header "Content-Type: application/json" \
  --data '{
  "connectionId": "$CONNECTION_ID",
  "arguments": {}
}'

The Authorization: Bearer <your MindCloud API Key> header authenticates you to MindCloud; the connectionId tells MindCloud which Atlassian MCP account to run the action against. Missing or invalid Authorization returns 401, and a missing or mismatched connectionId returns 400.

Set up a personal Atlassian API token for Atlassian MCP

This connection is for a personal scoped token created under your own Atlassian account. For machine-to-machine access, use the separate service-account auth option instead.

Create a scoped Atlassian token
In your Atlassian account, create a new API token and choose the Rovo MCP app. Select the scopes needed for the tools you want to run.
Enter your Atlassian email
Paste the email address for the Atlassian user who created the token into the Email field.
Enter the token value
Paste the scoped token into the API Token field and save the connection.
Run the session test
Use Atlassian MCP - Initialize Session to confirm the personal token can authenticate before testing tool calls.

Keep your key safe

Keep your MindCloud API Key on your server; do not ship it in browser code, mobile apps, public repositories, or logs. Anyone with the key can call the Universal API as your MindCloud account, across every connection you have created.