Microsoft Authenticator Limitations, Use Proton Authenticator
Two-factor authentication (2FA) is essential in helping to protect online accounts. But as more users adopt 2FA across dozens (sometimes hundreds) of accounts, the tools we rely on to manage these codes must scale with us.
Unfortunately, Microsoft Authenticator can’t fill the need for many power users. You may recall my other article on the limitations of Google Authenticator some time ago. I really thought I had something with Microsoft Authenticator, but I was wrong.
Don’t worry, the open source, privacy-first Proton Authenticator application has come to the rescue!
The Problem with Microsoft Authenticator
Microsoft Authenticator is widely used for generating time-based one-time passwords (TOTPs), but it comes with some frustrating limitations:
Code Quantity Limits
- There is a limit when trying to back up more than 100 accounts.
- Especially problematic for IT administrators managing multiple tenants or services.
Backup Size Restrictions
- The app also enforces a strict 5MB backup file size limit, regardless of your OneDrive or Microsoft 365 storage capacity. I mean, what the actual hell?!
- Once this limit is exceeded, users receive errors like “Backup too large” and are unable to sync their data to the cloud with no alternative solution provided.
- There’s no warning before hitting the limit—meaning users often discover the issue only when migrating to a new device.
Limited Export Options
- Microsoft Authenticator does not support full export/import of 2FA codes, making transitions between devices or platforms cumbersome.
These constraints can lead to serious headaches, especially when switching phones or trying to maintain a secure backup of all your 2FA tokens.
Enter Proton Authenticator: A Privacy-First, Scalable Alternative
Proton, the Swiss company behind Proton Mail and Proton Pass, recently launched Proton Authenticator—and it’s already turning heads.
Key Advantages Over Microsoft Authenticator
- Max Backup Size: No fixed limit
- Max Account Support: Scales with device storage
- Export/Import Support: Full import/export support
- Encrypted Sync: End-to-end encrypted
- Open Source: Yes
- Ads/Tracking: They say none, but I count displaying other Proton apps as Ads. However, I don’t mind.
- Cross-Platform (Desktop + Mobile): Full desktop + mobile
- Free to Use: Yes
Built for Privacy and Portability
- Proton Authenticator is open source and end-to-end encrypted, ensuring your 2FA codes are secure and private.
- It supports seamless import (for most codes) from other apps like Microsoft and Google Authenticator, making migration painless.
- Users can sync across devices without relying on proprietary cloud services—and without worrying about arbitrary backup limits.
No Strings Attached
- No Proton account required, unless you want it to sync across devices.
- No ads, no trackers, no paywalls.
- Available on Android, iOS, Windows, macOS, and Linux.
Conclusion
Microsoft Authenticator may still work well for casual end users, but its limitations are becoming increasingly problematic for those with complex security needs.
Proton Authenticator offers a refreshing alternative—one that respects your privacy, scales with your usage, and puts you in control of your data.
If you’re tired of hitting invisible ceilings and want a more transparent, secure, and user-friendly 2FA experience, Proton Authenticator might just be your next essential app.
As always, I welcome your thoughts, questions or suggestions on my article on the limitations of Microsoft Authenticator and recommendation to use Proton Authenticator instead.
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