5 Mistakes People Make When Setting Up Two-Factor Authentication

Fact-checked by the SnapMessages editorial team

Two-factor authentication mistakes are more widespread than most people realize, and they quietly undermine the security that 2FA is meant to provide. According to CISA’s guidance on multi-factor authentication, enabling 2FA reduces the risk of account compromise by more than 99% — but only when it is configured correctly.

With phishing attacks and SIM-swapping incidents rising sharply in 2025, getting your 2FA setup right is no longer optional. One misconfiguration can leave your accounts as exposed as having no protection at all.

Is SMS-Based Two-Factor Authentication Actually Safe?

SMS-based 2FA is the weakest form of two-factor authentication available, and relying on it is one of the most dangerous two-factor authentication mistakes you can make. Text message codes are vulnerable to SIM-swapping, where an attacker convinces your carrier to transfer your number to a device they control.

SIM-swap fraud has surged in recent years. The FBI’s Internet Crime Complaint Center reported that SIM-swapping complaints resulted in losses exceeding $48 million in a single year. Once an attacker controls your phone number, every SMS-based 2FA code you receive goes directly to them.

What to Use Instead of SMS

Authenticator apps like Google Authenticator, Authy, and Microsoft Authenticator generate time-based one-time passwords (TOTP) locally on your device. These codes are never transmitted over a cellular network, making them immune to SIM-swapping. For the highest security, hardware keys such as YubiKey from Yubico provide phishing-resistant authentication.

If you use messaging apps that handle sensitive conversations, understanding how authentication layers interact with the apps themselves is important. Our guide on end-to-end encryption explains the broader security stack that 2FA works within.

Are You Storing Your Backup Codes Correctly?

Ignoring backup codes is one of the most overlooked two-factor authentication mistakes, and it can lock you out of your own accounts permanently. Backup codes are single-use recovery codes provided when you first enable 2FA — they are your only lifeline if your primary authentication device is lost or damaged.

Most users dismiss the backup code screen during setup without saving the codes anywhere. Google, Apple, and Meta all provide one-time backup codes at enrollment, but they cannot be retrieved again after the initial setup screen closes. Losing these codes means a lengthy, often weeks-long account recovery process — if recovery is possible at all.

How to Store Backup Codes Safely

Print your backup codes and store them in a secure physical location, such as a locked drawer or safe. Alternatively, store them in a reputable password manager like 1Password or Bitwarden, which encrypts the data at rest. Never save them in an unencrypted notes app or screenshot folder on your phone.

Why Using One Device for Everything Is a Security Risk?

Storing both your password and your authenticator app on the same device defeats the entire purpose of two-factor authentication. The “two factors” in 2FA are meant to represent two independent, separate channels — something you know (password) and something you have (a separate physical device).

When your authenticator app lives on the same phone you use to log in, a single compromised or stolen device gives an attacker access to both factors simultaneously. This is a structural two-factor authentication mistake that is extremely common among users who set up apps like Google Authenticator or Authy without thinking about device separation.

The ideal setup uses a dedicated secondary device — such as a spare tablet — exclusively for your authenticator app, or relies on a hardware key as the second factor. This ensures that losing or compromising your primary device does not hand an attacker both authentication factors at once.

Can Phishing Steal Your Two-Factor Authentication Codes?

Yes — phishing attacks can and do bypass standard 2FA, making complacency about phishing one of the most critical two-factor authentication mistakes. Attackers use real-time phishing proxies, sometimes called adversary-in-the-middle (AiTM) attacks, to intercept both your password and your 2FA code the moment you enter them on a fake login page.

Tools like Evilginx2 allow attackers to operate a transparent proxy that mirrors a real login page. When you enter your credentials and your 2FA code, the attacker captures your authenticated session cookie — rendering your second factor useless. Microsoft’s Security Blog documented an AiTM phishing campaign that bypassed 2FA for over 10,000 organizations in a single operation.

The only authentication method that is fully resistant to this type of phishing is a FIDO2-compliant hardware key or passkey, because the cryptographic response is bound to the legitimate domain. No fake site can replicate it. If your accounts support passkeys — as Google, Apple, and GitHub now do — switching to them removes the phishing risk entirely. You should also stay aware of related threats like smishing attacks that use text messages to harvest your credentials before a phishing attempt even begins.

Are You Missing Critical Accounts That Need Two-Factor Authentication?

Selectively enabling 2FA only on your primary email while leaving other accounts unprotected is one of the most underestimated two-factor authentication mistakes. Attackers target peripheral accounts — cloud storage, social media, secondary email addresses — precisely because users assume those are lower-value targets.

Your secondary accounts often hold password reset permissions for your primary ones. A compromised Dropbox or LinkedIn account can be the entry point for a cascade attack that eventually reaches your bank. According to Verizon’s Data Breach Investigations Report, credential theft is involved in 86% of web application attacks — the majority of which exploit accounts where no second factor was ever configured.

Run a full audit of every account that holds personal data, financial access, or password-reset capabilities. Enable 2FA on all of them. If a service does not support 2FA, consider whether it is safe to store sensitive information there at all. For users who want to understand more about what spyware can access once an account is breached, our article on detecting and removing spyware from your phone covers the downstream risks. You should also understand how stalkerware gets installed to understand how account access enables deeper device-level compromise.

Frequently Asked Questions

What is the safest type of two-factor authentication to use?

FIDO2-compliant hardware keys, such as those from Yubico, are the most secure form of 2FA. They are immune to phishing, SIM-swapping, and real-time credential interception. Authenticator apps are a strong second choice for most users.

Can two-factor authentication be hacked?

Yes — SMS-based 2FA can be bypassed via SIM-swapping, and TOTP codes can be intercepted in adversary-in-the-middle phishing attacks. Only FIDO2 hardware keys and passkeys are considered fully phishing-resistant by security standards bodies like NIST.

What happens if I lose my two-factor authentication device?

You should use your pre-saved backup codes to regain access. If you did not save backup codes, you will need to go through the account provider’s identity verification process, which can take days or weeks. Always store backup codes securely before you need them.

Is using an authenticator app enough to stay secure?

An authenticator app is significantly more secure than SMS-based 2FA and protects against SIM-swapping. However, it does not protect against AiTM phishing attacks, which can capture your TOTP code in real time. For high-value accounts, combine an authenticator app with strong phishing awareness or upgrade to a hardware key.

Should I enable two-factor authentication on every account?

Yes. Every account that holds personal data, financial information, or password-reset capabilities for other accounts should have 2FA enabled. Attackers routinely exploit unprotected secondary accounts to access primary ones through credential chaining.

What are the most dangerous two-factor authentication mistakes for businesses?

For organizations, the most dangerous two-factor authentication mistakes include relying on SMS codes for employee accounts, failing to enforce 2FA policy across all users, and not training staff to recognize AiTM phishing pages. A single unprotected employee account can be the entry point for a full network breach.