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Administrators connect Atlassian once for the whole organization. After setup, each user connects their own Atlassian account, and their sessions can work with Jira through the official Atlassian MCP server.

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What this enables

Once a user connects their Atlassian account, agents in their sessions can:
  • search and read Jira issues, comments, and projects
  • create and update issues and add comments
  • use other consented Atlassian apps (for example Confluence) through the same connection
Agents act with the connecting user’s own Atlassian permissions.

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Requirements

  • You need the admin role in Cake Agents.
  • An Atlassian organization admin must authorize the Cake Agents domain before anyone can complete the Atlassian consent screen. Cake identifies itself to Atlassian with a Client ID Metadata Document hosted on its own domain, and Atlassian blocks consent from custom domains until an admin allows them:
    1. Go to Atlassian Administration and select your organization.
    2. Select Connectors, then Atlassian MCP server.
    3. Select Add domain and add the domain of your Cake Agents deployment — the host of the URL you use to open Cake Agents, for example cake-agents.example.com.
    Domain settings apply to the whole Atlassian organization. OAuth 2.1 is Atlassian’s default authentication method for the MCP server, so no other connector setting needs to change.
  • Each user needs access to the Atlassian site they select at consent.

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Instructions

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Add the Atlassian MCP server

  1. In Cake Agents, go to Settings → Organization → MCP Connectors.
  2. Under Add an MCP server, enter:
    • Name: atlassian — this prefixes the tools agents see, for example atlassian.search. Pick a short, unique name; see Choose a name.
    • URL: https://mcp.atlassian.com/v2/mcp — the canonical Atlassian MCP endpoint. Older v1 URLs are not supported.
  3. Select Add server. Cake contacts Atlassian and registers itself as an OAuth client before saving; if registration fails, Cake shows the reason and does not save the server.

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Connect user accounts

Each user then connects their own Atlassian account in Settings → User → MCP Connectors. See Connect to MCP servers. At consent, the user picks their Atlassian site and approves the requested permissions.
Cake requests the scopes the Atlassian MCP server advertises, so the consent screen spans multiple Atlassian apps and includes write, manage, and delete permissions. There is no Jira-only isolation.
When a user messages a session, the agent can call Atlassian tools through the Cake MCP server. The agent uses the connections of the last user who sent a message to the session; if nobody has sent a message yet, it uses the session creator’s connections.

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Remove the integration

Removing the Atlassian server in Settings → Organization → MCP Connectors deletes every user’s saved Atlassian connection. Re-adding the server requires every user to connect again. A user can disconnect only their own account in Settings → User → MCP Connectors without affecting anyone else.

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Troubleshooting

The Cake Agents domain is not authorized in your Atlassian organization, or an org policy blocks the connection. Add the domain under Atlassian Administration → Connectors → Atlassian MCP server → Domains (see Requirements), and check the user’s site access and the org’s OAuth and IP-allowlist policies.

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Registration fails or tools never appear after a v1 URL was used

Only the canonical v2 endpoint https://mcp.atlassian.com/v2/mcp is supported. If the server was registered with a v1 URL, remove it in Settings → Organization → MCP Connectors and add the v2 URL instead; users then reconnect their accounts.

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No Atlassian tools in a session

The user has not connected their own Atlassian account — org registration alone is not enough. Connect in Settings → User → MCP Connectors. Transient Atlassian throttling can also interrupt consent or tool calls; retry before changing configuration.

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Not supported

Jira events cannot start Cake sessions — the Atlassian MCP server exposes tools only, with no webhook channel. For issue-triggered sessions, see Set up Linear.