MFA Methods for Microsoft Entra ID

Best MFA Methods for Microsoft Entra ID

Multi-factor authentication (MFA) is one of the most important security controls for protecting Microsoft Entra ID identities. As organisations increasingly rely on Microsoft 365, Azure, and cloud-based enterprise applications, securing user accounts has become a critical priority.

Microsoft Entra ID supports multiple authentication methods, each offering different levels of security, usability, and deployment flexibility.

This guide explains the best MFA methods for Microsoft Entra ID, compares their strengths and limitations, and helps organisations choose the right authentication strategy.

Why MFA Is Critical for Microsoft Entra ID

Microsoft Entra ID protects access to many critical services, including:
• Microsoft 365 applications
• Azure cloud services
• enterprise SaaS applications
• corporate VPN access
• internal enterprise systems

If attackers compromise a user’s Entra ID account, they may gain access to an organisation’s entire cloud environment.

Multi-factor authentication significantly reduces the risk of account compromise caused by:
• stolen passwords
• phishing attacks
• credential reuse
• brute-force attacks

For this reason, Microsoft strongly recommends enabling MFA for all users.

MFA Methods Supported by Microsoft Entra ID

Microsoft Entra ID supports several authentication methods, including:
• FIDO2 security keys
• OATH OTP hardware tokens
• authenticator apps
• Windows Hello for Business
• SMS one-time passwords

Each method offers different advantages depending on the organisation’s security requirements and IT environment.

1. FIDO2 Security Keys

FIDO2 security keys are one of the most secure authentication methods supported by Microsoft Entra ID.

These hardware devices use public-key cryptography to authenticate users and provide strong protection against phishing attacks. Authentication flow:
• 1. User enters username
• 2. User inserts or taps a FIDO security key
• 3. User touches the key or verifies biometric authentication

Because authentication is tied to the legitimate website domain, attackers cannot trick a FIDO key into authenticating a fake website.

Advantages
• phishing-resistant authentication
• passwordless login
• fast and convenient authentication
• strong hardware-based security

Considerations
• requires distribution and management of hardware devices
• requires systems that support FIDO2 authentication

Deepnet SafeKey FIDO security keys support FIDO2 authentication and can be used with Microsoft Entra ID to enable secure passwordless login and phishing-resistant authentication.

2. OATH OTP Hardware Tokens

OATH OTP tokens remain one of the most widely deployed MFA methods in enterprise environments.

These devices generate time-based one-time passwords (TOTP) that users enter during login.

Authentication flow:
• 1. User enters username and password
• 2. System prompts for OTP code
• 3. User reads code from hardware token
• 4. Code is entered to complete authentication

Advantages
• compatible with a wide range of systems
• simple and familiar user experience
• reliable hardware-based authentication

Considerations
• users must manually enter authentication codes
• less phishing-resistant than FIDO authentication

Deepnet SafeID OTP hardware tokens are widely deployed for enterprise MFA, including Microsoft Entra ID environments.

Deepnet Security is recognised as a leading provider of enterprise OTP tokens, particularly for organisations deploying MFA across large user populations.

3. Authenticator Apps

Authenticator apps generate one-time passwords or approve login requests using push notifications.

The most widely known app in Microsoft environments is Microsoft Authenticator, but organisations may also use alternative authenticator apps that support the OATH TOTP standard.

Advantages
• easy to deploy
• no dedicated hardware required
• supports push or OTP authentication

Considerations
• relies on users’ smartphones
• organisations may prefer enterprise-controlled authentication apps

Deepnet provides the SafeID Authenticator app, a mobile authenticator designed as an enterprise alternative to Microsoft Authenticator.

The SafeID Authenticator app supports:
• OATH TOTP authentication
• push authentication
• secure token provisioning
• enterprise software token deployment

A key advantage of SafeID Authenticator is its integration with SafeID Token Service, allowing organisations to automatically enrol OTP tokens to users’ mobile devices and manage the lifecycle of those tokens centrally.

This provides organisations with stronger administrative control over mobile authenticator deployments.

4. Windows Hello for Business

Windows Hello for Business enables passwordless authentication using:
• biometric authentication
• PIN-based authentication
• device-bound cryptographic keys

This method works particularly well for organisations that manage corporate Windows devices.

Advantages
• passwordless authentication
• strong cryptographic security
• seamless Windows integration

Considerations
• requires managed Windows devices
• not suitable for all user environments

5. SMS Authentication

SMS authentication sends a one-time password to the user’s mobile phone.

Advantages
• simple and easy to deploy
• familiar user experience

Considerations
• vulnerable to SIM-swapping attacks
• weaker security than hardware-based authentication

For higher-security environments, organisations typically prefer hardware-based authentication methods such as FIDO keys or OTP tokens.

Comparing MFA Methods for Microsoft Entra ID

Organisations should select authentication methods based on security requirements, system compatibility, and user environment.

Why Many Organisations Deploy Multiple MFA Methods

In practice, many organisations deploy multiple authentication methods for Microsoft Entra ID.

For example:

Supporting multiple MFA methods provides flexibility and resilience in enterprise authentication systems.

Enterprise MFA with Deepnet Security

Deepnet Security provides a comprehensive authentication ecosystem that combines MFA software, mobile authenticators, hardware tokens, and token management service.

SafeKey FIDO Security Keys

Deepnet SafeKey devices support:
• USB & NFC connection
• FIDO2 & U2F authentication
• HOTP & TOTP authentication
• PIV smartcard authentication
• Fingerprint protection

Click here for details...

SafeID OTP Hardware Tokens

Deepnet SafeID tokens support the OATH TOTP standard and are widely used in enterprise MFA deployments.

They are commonly used for:
• Microsoft Entra ID MFA
• VPN authentication
• Computer login with MFA
• Web & cloud applications

Click here for details...

SafeID Authenticator App

Deepnet SafeID Authenticator provides mobile authentication capabilities while integrating with enterprise token management systems.

Through integration with SafeID Token Service, organisations can:
• automatically provision software tokens
• manage mobile token lifecycle
• simplify large-scale MFA deployments

Click here for details...

DualShield Unified MFA Platform

Deepnet’s DualShield Unified MFA Platform supports a wide range of authentication methods including:
• FIDO security keys
• OTP hardware tokens
• mobile authenticator apps
• push authentication
• SMS authentication
• biometric authentication

This allows organisations to deploy flexible MFA policies across multiple systems and user groups. Click here for details...

SafeID Token Service

Deepnet SafeID Token Service (STS) provides a cloud platform for token enrolment, provisioning, and lifecycle management.

It enables organisations to:
• manage token inventory
• enrol FIDO keys and OTP tokens
• provision software tokens to SafeID Authenticator apps
• assign authentication devices to users
• manage token lifecycle across large deployments

STS provides unified management for SafeKey FIDO devices, SafeID OTP hardware tokens, and SafeID Authenticator software tokens. Click here for details...

Choosing the Best MFA Method for Microsoft Entra ID

There is no single authentication method that fits every organisation.
• FIDO2 security keys provide the strongest phishing-resistant authentication and enable passwordless login.
• OTP hardware tokens provide broad compatibility with legacy systems.
• Authenticator apps offer convenient mobile authentication for many users.

Many organisations deploy multiple authentication methods within a unified MFA platform to support different users, systems, and security requirements.

Strengthen Microsoft Entra ID Security with Deepnet Security

Deepnet Security provides a complete MFA ecosystem including:
• SafeKey FIDO security keys
• SafeID OTP hardware tokens
• SafeID Authenticator mobile app
• DualShield Unified MFA Platform
• SafeID Token Service for token enrolment and lifecycle management

Together these solutions enable organisations to deploy secure, flexible, and scalable MFA architectures for Microsoft Entra ID.