How to log in with 2FA for Jira using U2F device as authentication second factor?

After you added an account in your authenticator application you don't need to scan QR code again. All you have to do is:

Step 1. Log in with your credentials (username and password) as usual. The second-factor authentication page will open.

Now you have 3 options:

1 Option. Plug your U2F device in, click Submit, and press the button on the device.

2 Option. In case you don't have your U2F device you can use your mobile authenticator app. Click Enter a two-factor code from your phone. Find out How to log in using your phone here.

3 Option. In case you have neither U2F device nor mobile authenticator (phone) you can use backup (recovery) codes and enter a one-time secret reserve key.