Google and Microsoft Authenticator Aren't the Best Choice

An authenticator app stores one secret for each account you protect with two-factor authentication. This seed secret is what the app turns into the short TOTP codes you type at sign-in. Whoever has the secret can make the same codes as your phone.

Google Authenticator and Microsoft Authenticator are free apps from Google and Microsoft. Three questions show where other apps do more: who can read the secrets once they leave the phone, what it costs to move to another app, and whether anyone outside the company can check the code. The apps used for comparison are Aegis, Ente Auth and Proton Authenticator.

Google Authenticator works without any account [1]. Microsoft Authenticator makes codes without an internet connection, and besides codes it approves sign-ins to Microsoft accounts [8].

Who can read the copy of your codes

The first question is key custody: once a copy of your secrets leaves the phone, who holds the key that opens it? Google released Google Authenticator in 2010, and until April 2023 the codes lived on one device, so a lost phone meant losing sign-in to every service set up with it [2]. Syncing to a Google Account fixed that and put a copy of the secrets on Google’s servers.

Google’s help page says Google “encrypts Authenticator codes both in transit and at rest” [1]. Encryption at rest protects a copy against a stolen disk, not against whoever holds the keys. The page describes no end-to-end encryption and no key or passphrase that you hold [1].

In April 2023, researchers at Mysk reported that the sync traffic is not end-to-end encrypted. Google’s group product manager answered that the company plans to offer end-to-end encryption “in the future”, and pointed to the risk that it can leave users “locked out of their own data without recovery” [3]. Google’s help page still describes only encryption in transit and at rest [1].

A synced copy also means that whoever gets into your Google account gets your codes. On 27 August 2023, an attacker phished an employee of the software company Retool, got one code over the phone and reached the employee’s Google account, which held the employee’s synced codes. Retool called this “a novel attack vector” and “the major reason” the attacker got in; 27 of its cloud customers had their accounts accessed [4]. It was a breach of Retool through a Google account, not a flaw in the app or a breach of Google.

In the “Use without an account” mode, the codes stay on the phone and are removed from your Google Accounts, and the page describes no backup file for that mode [1].

The backup in Microsoft Authenticator is a copy you can set up. Microsoft’s help page describes it as stored with a Microsoft personal account you choose on Android and in iCloud on iPhone, and says that from January 2027 Android backup moves to Google One backup [7]. Per Microsoft’s 2019 description, the app requests a 256-bit key from an internal Microsoft account key service, encrypts your accounts with it, including the shared secrets behind time-based codes, and uploads the result. To restore, the app fetches the same key from the same service [6]. The description names no password or key of your own, so under this design Microsoft holds the key. Microsoft’s current support pages do not describe the encryption, including that of the iCloud copy and of the Google One backup [7].

A backup made on an iPhone cannot be restored on Android, and work or school accounts are not backed up: only the account name is saved [7].

The other three apps answer differently. Aegis can keep its vault in plain text or encrypt it with AES-256 under a random master key that a key derived from your password locks, and its documentation describes storage on the phone only, with no account or cloud sync [9]. Aegis declares no internet permission [10], so it cannot send anything over the internet by itself. Ente says its servers store only encrypted copies of your codes and master key and cannot read the codes or your password [11]. Proton says that when you turn on sync, Proton Authenticator creates a random key and encrypts it with your Proton account key, “ensuring only you can decrypt it”, and that Proton’s servers never have access to unencrypted data [13].

What it costs to leave

Moving to another app means taking the secrets with you, and an export is the file that carries them. Google describes one way to move codes, a QR-code transfer between devices [1]. Google documents no backup file and no other export.

Microsoft’s FAQ and backup page describe no export of one-time codes; the only export topic in the FAQ is passwords [8]. The backup restores only into the same app on the same kind of phone [7].

Ente Auth, for comparison, exports your codes into a file encrypted with a separate export password, and Ente says it cannot recover that password for you [12]. How Aegis and Proton Authenticator handle export is covered in their reviews.

Whether anyone can check the code

Open source code lets anyone read how an app stores and encrypts the secrets. Both big apps are closed. Google once published an open-source fork of the Android app; the fork was archived in June 2020, and its README says “the official version of the app still remains proprietary” [5]. Microsoft Authenticator is closed source too. Outsiders cannot read the source code of either app.

Aegis publishes its code on GitHub [9], Ente says its apps are open source [11], and Proton Authenticator publishes the code of its Android app on GitHub [19]. Published code makes outside checks possible; it does not mean anyone has done them.

The comparison at a glance

	Google Authenticator	Microsoft Authenticator	Aegis	Ente Auth	Proton Authenticator
Key of your own for the synced copy	No	No	No synced copy	Yes	Yes
Backup or sync through	Google Account	Microsoft account or iCloud	Backup file you set up	Ente account	Proton account
Code is public	No	No	Yes	Apps	Android app

Want every field side by side? Open the full comparison.

What has gone wrong in the apps

Problems are not limited to the two big apps. Microsoft published three security advisories for Microsoft Authenticator in 2026, in March, May and September, two for information disclosure and one for elevation of privilege; Microsoft marked none of them as exploited or publicly disclosed [16][17][18]. Aegis had a High-rated advisory in September 2026: a crafted icon pack could overwrite Aegis’s internal files, including the vault, if you imported it, and version 3.4.3 fixes it [15]. A week after Proton Authenticator launched, in August 2025, its iOS app was found to write full secrets to its debug logs in plain text; Proton shipped a fix the same day. Proton said this was not a vulnerability an attacker could exploit, because the logs are local only; the report notes the risk if a user shares the logs [14].

Where these apps still make sense

In the “Use without an account” mode, Google Authenticator keeps the secrets on one device and no copy exists for a stolen Google account to reach. A copy locked with a key only you hold has its own cost: if you forget the password, nobody can open the copy for you. Google’s product manager named this risk when explaining why end-to-end encryption would come later [3].

For someone who signs in to a Microsoft account, Microsoft Authenticator is also the app that approves those sign-ins.

Other apps to look at

Aegis suits an Android user who wants the secrets on the phone and nowhere else: it is account-less and has no internet permission. The trade-off is that you make and keep your own backups; at setup Aegis can also store the vault in plain text [9], and a lost phone with no backup means recovering each account at its own service. See Aegis vs Google Authenticator.

Ente Auth suits someone who wants the same codes on Android, iOS, Windows, macOS, Linux and the web, with a synced copy Ente says it cannot read. An account is optional: without backup, the codes stay on the device [11]. The trade-off is a recovery key you have to keep: it is the way back in after a forgotten password. See Ente Auth vs Microsoft Authenticator.

Proton Authenticator suits someone who already has a Proton account; without sync, the app also stores codes with no account [13]. The trade-off is that sync goes through a Proton account, and the iOS app logged full secrets in its first week [14]. See Google Authenticator vs Proton Authenticator.

Summary

Google encrypts the synced copy of your secrets in transit and at rest and offers no key of your own, and Microsoft’s backup, per its 2019 description, uses a key from a Microsoft service. Google describes only a QR transfer, Microsoft describes no export of codes, and neither app’s code is public. Aegis, Ente Auth and Proton Authenticator do more on at least one of these points, in exchange for backups you manage yourself, a recovery key you keep, or sync through a Proton account. Microsoft Authenticator, Aegis and Proton Authenticator have each had a documented bug, so this compares design, not clean records.