Error making tool calls to Rovo MCP Server

Question

We are using the official Atlassian Rovo MCP Server -

We have a custom MCP client and when we make a tool call to the Rovo MCP server after successfully authenticating , we see an error when making a tool call from the client. This is after the user sucessfully authenticates as well as provides the necessary authorization including the scopes.

Failed to call tool: {"meta":null,"content":[{"type":"text","text":"{\"error\":true,\"message\":\"We couldn't verify your access. Reconnecting and signing in again may resolve this issue.\"}","annotations":null,"meta":null}],"structuredContent":null,"isError":true}

"message_parsed": {
"connector_id": "cnb-jira-oauth-51fpu9",
"err": "oauth: no refresh token in connector data",
"level": "ERROR",
"msg": "failed to refresh identity",
"request_id": "e04927d5-b537-44e1-ac27-eb43c78a6313",
"source": {
"file": "/usr/local/src/dex/server/refreshhandlers.go",
"function": "github.com/dexidp/dex/server.(*Server).refreshWithConnector",
"line": 344
},
"time": "2026-08-10T19:08:11.183Z",
"user_id": "1f5fd952-1054-4431-ac2e-615d269c32f1"
},

Additionally, we would also like to know where and how we can see all the Rovo MCP Server generated logs and telemetry - currently we are unable to see those. Please help with this ASAP

Thanks!

James Gamble · Answer

Hola Shivam,

The two URLs serve different purposes.

For your custom MCP client, keep https://mcp.atlassian.com/v1/mcp/authv2 configured as the MCP server endpoint.

For the OAuth authorization endpoint, I wouldn’t hard-code https://auth.atlassian.com/authorize. Instead, have the client follow Atlassian’s OAuth discovery flow. For the authv2 MCP endpoint, the protected-resource metadata is available here.

That metadata should lead the client to the current authorization server and its authorization/token endpoints. Atlassian’s current changelog documents the discovery behavior here.

Given the refresh-token behavior you’re troubleshooting, I’d check specifically whether your custom client is performing that discovery rather than using a statically configured authorization URL.

Thanks,

James

Shivam.Saith · Answer

Thanks James - quick clarification - should we use https://mcp.atlassian.com/v1/mcp/authv2 as the Authorization URL that our custom MCP client needs or should that be

https://auth.atlassian.com/authorize

I've seen some conflicting information online around this - hence the confusion

Best,
Shivam

James Gamble · Answer

Hola Muntaser,

I don’t see offline_access listed in Atlassian’s published Rovo MCP guidance as a required scope for custom clients, so adding it isn’t expected to fix the issue on its own.

The important part is that you’re still getting “oauth: no refresh token in connector data” even after requesting offline_access. That suggests the problem is with the refresh token not being issued or retained correctly, rather than with that scope simply being absent.

At this point, I’d verify that your client is following Atlassian’s documented OAuth 2.1 flow exactly and, if the same error persists, raise it with Atlassian Support so they can determine whether the refresh token is being omitted during issuance or lost when the connector state is stored.

Thanks,

James