Hello Snorre,
Thanks for reaching out to us.
Yes, since scanning the QR code isn’t really an option to set up 2FA in the desktop app, you can inform your users to copy the SECRET KEY which is present below the QR code during the process of registration/configuration and paste it on the “Enter Code given by the website” text box present in the add account section (marked with “+” sign on the top right corner of the Authy desktop app).
Paste the SECRET KEY, click on add account and select an account name and logo for this 2FA registration.
Once you are done with the above-mentioned steps a 2FA passcode will be visible in the Authy Desktop app against your added account.
Users can use this passcode to validate themselves while they log into their respective Jira accounts.
I hope I was able to clear your doubt.
Let me know if you have any more concerns.
Thanks,
Aniket Sarkar