Issue Summary

POP3 doesn’t work after upgrading Jira to 9.12.27 because “POP3: mail.pop3s.auth.xoauth2.two.line.authentication.format: false" even though we have this checkbox ticked

Steps to Reproduce

1. Upgrade to install Jira version 9.12.27
2. Create application links to use OAuth2 with Microsoft Azure, following this documentation: Integrating OAuth 2.0 for Microsoft Accounts on Jira and Jira Service Management
3. Now, try configuring an incoming mail with SECURE_POP and POP3 protocol; it throws an error stating

Expected Results

The authentication should work fine

Actual Results

As per this bug

https://jira.atlassian.com/browse/JRASERVER-72033#:~:text=For%20the%20combination%20POP%20+%20Oauth,versions%20which%20introduced%20the%20fix:

It’s required for POP3 to use the box Use two-line authentication format. For the combination POP + Oauth 2.0 to work in the fixed Jira versions, it is necessary to tick the box Use two line authentication format in the Mail Server configuration before clicking on Test Connection, as shown in the screenshot below.
 
Note that this new setting is only available in the Jira versions that introduced the fix:
 
But even if we check this box the debug logs still says that Jira is using the single line authentication, but not the two-line authentication

2025-10-06 15:21:27,361+0000 DEBUG [test oauth] http-nio-8080-exec-11 url: /jira/secure/admin/VerifyPopServerConnection!add.jspa; user: admin admin 921x709x1 4pcm2f 10.140.13.100,172.50.0.5 /secure/admin/VerifyPopServerConnection!add.jspa DEBUG POP3: mail.pop3s.auth.xoauth2.two.line.authentication.format: false 2025-10-06 15:21:31,828+0000 DEBUG [test oauth] http-nio-8080-exec-11 url: /jira/secure/admin/VerifyPopServerConnection!add.jspa; user: admin admin 921x720x1 4pcm2f 10.140.13.100,172.50.0.5 /secure/admin/VerifyPopServerConnection!add.jspa DEBUG POP3: mail.pop3s.auth.xoauth2.two.line.authentication.format: false 2025-10-06 15:21:32,751+0000 DEBUG [test oauth] http-nio-8080-exec-11 url: /jira/secure/admin/VerifyPopServerConnection!add.jspa; user: admin admin 921x720x1 4pcm2f 10.140.13.100,172.50.0.5 /secure/admin/VerifyPopServerConnection!add.jspa DEBUG POP3: mail.pop3s.auth.xoauth2.two.line.authentication.format: false root@9162b976b1fb:/var/atlassian/application-data/jira/log#

It works in Jira 9.12.24 but not in 9.12.27.

Workaround

Currently there is no known workaround for this behavior. A workaround will be added here when available