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How to Set Up MFA for a Small Business (Including Microsoft 365)

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Who this is for: Small business owners who want to turn on multifactor authentication (MFA) for email, banking, and other business accounts, including Microsoft 365.

About 45 minutes for your own and your admin accounts (rolling it out to staff takes longer)Easy

Flat illustration of a laptop sign-in screen showing a two-digit number, a phone with an authenticator prompt asking for that number, and a USB security key, next to a shield with a checkmark

Multifactor authentication (MFA) means you need two things to sign in: your password plus something else, like an app on your phone, a security key, or your fingerprint. If a criminal steals or guesses your password, they still can't get in without that second factor (CISA). You may also see it called two-factor authentication, 2FA, or 2-step verification. They all mean the same idea.

Not all MFA is equally strong. CISA ranks the options from strongest to weakest (CISA fact sheet):

Any MFA is better than none (CISA). Turn on what you can today, then move up the list.

Compare methods
Option How strong Why
Passkeys and security keys (FIDO2/WebAuthn)Best ("phishing-resistant")A fake login page can't trick them into working.
Authenticator app with codes, or push with number matchingGoodStops "keep tapping Approve" attacks, but a code you type can still be phished.
Push approval without number matchingWeakerVulnerable to prompt-spamming ("MFA fatigue").
Text message (SMS) or voice codesLast resortVulnerable to phishing, SIM swaps, and phone-network attacks.
  1. Part 1: MFA basics for any business

  2. List the accounts that matter most

    Done when: I have a list of the business accounts that need MFA, with email at the top.

    Start with the accounts a criminal would most want. CISA urges MFA for all users and all services, including email, file sharing, and financial accounts (CISA fact sheet). It also names remote access and billing systems (CISA). A typical small business list:

    • Business email (Microsoft 365 or Google Workspace)
    • Bank, payroll, and accounting software
    • Your website, domain name, and hosting accounts
    • Remote access tools and file sharing
    • Business social media accounts
  3. Protect admin accounts first

    Done when: Every admin account has MFA, uses the strongest method available, and is used only for admin work.

    Admin accounts can change everything, so do them first. CISA strongly urges system administrators and other high-value targets to use phishing-resistant MFA, or plan to move to it (CISA fact sheet). In Microsoft 365, keep Global Admins to fewer than five, use separate admin accounts for admin work, and keep two secured emergency ("break-glass") accounts (Microsoft Learn; Microsoft Learn). Part 2 covers how.

  4. Use an authenticator app instead of text messages

    Done when: Staff use an authenticator app (or a passkey) instead of text-message codes wherever the account allows it.

    Text and voice codes can be stolen through SIM swaps, where a criminal talks your phone carrier into moving your number to their phone, and through weaknesses in the phone network. CISA calls SMS a last-resort option (CISA fact sheet). NIST lists phone-network delivery (SMS or voice) as a "restricted" method with extra risk (NIST SP 800-63B-4, Sec. 3.1.3.3 and 3.2.9). CISA calls app-based codes, or push with number matching, the best options for small and mid-size businesses that can't move to phishing-resistant MFA right away (CISA fact sheet).

    After you switch, check whether text messages are still turned on as a backup. CISA's guidance for highly targeted people notes that adding an app doesn't automatically remove SMS from an account, so the weak option stays as a fallback until you turn it off (CISA mobile guidance). Some services fall back to SMS for account recovery, and you may not be able to turn that off.

  5. Make sure push approvals use number matching

    Done when: Any "approve sign-in" app prompts make users type or pick the number shown on the sign-in screen.

    With plain push MFA, an attacker who has the password can send prompt after prompt until someone taps Approve to make them stop. CISA calls this "MFA fatigue" or "push bombing." Number matching blocks it: the sign-in screen shows a number, and you must enter it in the app to approve (CISA number matching fact sheet). NIST no longer considers plain "approve" prompts acceptable for the same reason (NIST SP 800-63B-4, Sec. 3.1.3). Microsoft Authenticator now uses number matching for all push notifications (Microsoft Learn). For other apps, look for a setting called number matching or verified push.

  6. Move admins and key accounts to passkeys or security keys

    Done when: Admins, and anyone who can move money, sign in with a passkey or security key where the service supports it.

    Passkeys and security keys use the FIDO2/WebAuthn standard. CISA calls this the only widely available phishing-resistant authentication, because it won't work on a fake login site (CISA). It can be a small USB or NFC key, or it can be built into a laptop or phone (CISA fact sheet). NIST explains why codes fall short: anything you type in by hand, like a six-digit code, can be passed along by a fake site, so it isn't phishing-resistant (NIST SP 800-63B-4, Sec. 3.2.5).

    Start with your admin accounts and the people who approve payments, then add others over time.

  7. Set up a backup way to sign in

    Done when: Each person has a second sign-in method registered, and recovery codes are stored somewhere safe.

    Phones get lost and keys break. NIST recommends keeping at least two separate ways to sign in, so a lost device doesn't lock you out (NIST SP 800-63B-4, Sec. 4.1.2.1). For example, register a second security key or a passkey on another device. Many services also give you one-time recovery codes. Store those somewhere safe, away from the device they back up.

  8. Teach your team about MFA fatigue

    Done when: Everyone knows to deny any sign-in prompt they didn't start, and to report it right away.

    An MFA prompt you didn't ask for means someone may already have your password. CISA recommends training staff to recognize MFA spam and report unexpected prompts, and having someone look into denied requests, since they can mean the password has been stolen (CISA number matching fact sheet). The rule for staff is simple:

    1. Never approve a prompt or share a code you didn't ask for.
    2. Tell your manager or IT contact right away.
    3. Change that account's password.
  9. Require MFA for everyone, with no exceptions

    Done when: MFA is required for every employee and contractor, not just the ones who opted in.

    The FTC tells businesses to require MFA for all employees, contractors, and others who access your network and devices (FTC Small Business). CISA lists requiring MFA as one of four essential steps for small businesses, using phishing-resistant MFA where available (CISA). Don't make exceptions for "the boss" or for shared accounts. If a system can't do MFA, CISA recommends planning to upgrade or replace it (CISA fact sheet).

  10. Part 2: Microsoft 365

    These steps pair with steps 1 and 2 of our Microsoft 365 Business Premium Setup Checklist. You'll work in the Microsoft Entra admin center (entra.microsoft.com). Menu names below are from Microsoft's documentation as of October 2026 and may move.

  11. Check that security defaults are on (any Microsoft 365 plan)

    Done when: Security defaults are on, or Conditional Access policies are doing the same job.

    Security defaults are Microsoft's free, built-in MFA settings. They require everyone to register for MFA, require admins to use MFA, prompt other users when Microsoft sees a need, and block old sign-in methods that can't do MFA (Microsoft Learn). Microsoft 365 organizations created after October 2019 have them on by default (Microsoft Learn).

    To check: go to Entra ID > Overview > Properties > Manage security defaults (Microsoft Learn). Have staff register at myprofile.microsoft.com under Security info. Security defaults use the Microsoft Authenticator app with notifications, and staff can also use codes from other authenticator apps (Microsoft Learn).

    Microsoft is also requiring MFA to sign in to its admin portals. Enforcement began in October 2024 for the Entra admin center and in February 2025 for the Microsoft 365 admin center, rolling out gradually to all tenants (Microsoft Learn).

  12. Create two emergency access ("break-glass") accounts

    Done when: There are two cloud-only emergency admin accounts with passkeys or security keys, stored safely and tested.

    Before you tighten anything, make sure you can't lock yourself out. Microsoft recommends two or more emergency access accounts (Microsoft Learn):

    • Cloud-only accounts on your .onmicrosoft.com domain, with the Global Administrator role
    • Not tied to any one person, and used only in an emergency
    • Signed in with a passkey/security key (FIDO2) or certificate-based authentication
    • Kept out of Conditional Access policies that block or restrict sign-in
    • Credentials stored safely, sign-ins monitored, and tested at least every 90 days

    Microsoft's required admin-portal MFA applies to these accounts too. A passkey or certificate-based sign-in meets that requirement (Microsoft Learn).

  13. With Business Premium, switch to Conditional Access

    Done when: The four baseline Conditional Access policies are on, with only the emergency accounts excluded, and security defaults are off.

    Business Premium includes Microsoft Entra ID P1, which adds Conditional Access, a more flexible way to require MFA. You can't use security defaults and Conditional Access together (Microsoft Learn). Turn security defaults off only when your Conditional Access policies are ready to replace them. Microsoft's steps (Microsoft Learn):

    1. Get ready first: create your emergency access accounts (Step 10) and have admins register passkeys or security keys. Then turn off security defaults and create the policies below right away, so you're never left without MFA.
    2. Go to Conditional Access > Policies > New policy from template and create these four policies from the Secure foundation templates: Require MFA for all users, Require MFA for administrators (or the stronger Require phishing-resistant MFA for administrators), Block legacy authentication, and Require MFA for Azure management.
    3. Fix the exclusions. Each new policy automatically excludes the account you created it with. Remove that account and exclude only your emergency access accounts.

    If you choose the phishing-resistant admin policy, have your admins register passkeys or security keys first. Microsoft warns that skipping this can lock you out, and recommends starting the policy in Report-only mode before turning it on (Microsoft Learn).

  14. Turn on passkeys for your staff

    Done when: Passkeys (FIDO2) are enabled in the Authentication methods policy.

    Passkeys work in every Microsoft Entra edition with no extra license. To turn them on, go to Entra ID > Security > Authentication methods > Policies > Passkey (FIDO2) and allow self-service setup. Staff can then use a security key, a passkey in Microsoft Authenticator, or a synced passkey such as Apple or Google's (Microsoft Learn). Microsoft lists passkeys, FIDO2 security keys, Windows Hello for Business, and certificate-based authentication among its phishing-resistant options (Microsoft Learn).

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Don't count on these

  • Text-message codes as your long-term answer. They're better than nothing, but CISA calls them a last resort (CISA fact sheet).
  • Codes sent by email. NIST says email shouldn't be used for this kind of sign-in check, because anyone with the email password can read the code (NIST SP 800-63B-4, Sec. 3.1.3.1). (Some guides, including the FTC's, still list email codes as MFA; NIST's newer guidance says not to.)
  • Security questions ("What was your first pet's name?"). NIST says services shouldn't use them when you choose a password (NIST SP 800-63B-4, Sec. 3.1.1.2).
  • Thinking any MFA stops phishing. A fake login page can collect your password and the six-digit code together. Only passkeys and security keys block that (CISA fact sheet).
  • Legacy "per-user MFA" in Microsoft 365. Microsoft recommends security defaults or Conditional Access instead (Microsoft Learn).

Keep it up

Put a quarterly reminder on your calendar. Check that new hires are set up with MFA, remove departed staff, confirm admins still use their strongest method, and test the emergency access accounts (Microsoft says at least every 90 days) (Microsoft Learn).

Sources

Checked on October 11, 2026.

Microsoft, Microsoft 365, Entra, and Microsoft Authenticator are trademarks of the Microsoft group of companies. FIDO and FIDO2 are trademarks of the FIDO Alliance. Hawkcrest Cyber is an independent consultancy and isn't affiliated with Microsoft or any agency cited here.

Want us to do this for you?

Hawkcrest Cyber can roll out MFA across your business without locking anyone out: security defaults or Conditional Access, emergency access accounts, passkeys for your admins, and a plain-English guide for your staff. I'm Cory Zaner, a Houston-area cybersecurity architect (CISSP, CISM) and U.S. Air Force veteran.

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