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Conditional Access

How to Secure Microsoft 365: A Practical Admin Baseline

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Secure Microsoft 365 by requiring multifactor authentication (MFA), choosing either security defaults or a carefully designed Conditional Access baseline, preserving emergency access, and applying email and device protections that fit your tenant. No single setting or score secures the whole environment: confirm licensing and dependencies, test policy changes, and review the controls regularly.

Start with identity protection and recovery

Require MFA broadly

Microsoft recommends requiring MFA for all users. Its guidance describes three built-in authentication strengths: standard multifactor authentication, passwordless MFA, and phishing-resistant MFA. The phishing-resistant option is the most restrictive of the three. Microsoft lists FIDO2 security keys, Windows Hello for Business or platform credentials, and multifactor certificate-based authentication among the combinations that satisfy this strength.

A FIDO2 security key is one possible method, not a complete security solution. Confirm that the method is enabled for the relevant users, works with their devices, and is required by the policies that protect the access you care about. Use phishing-resistant methods for higher-risk accounts or sensitive access when your environment supports them.

Microsoft’s guidance quotes Alex Weinert, its Director of Identity Security, saying: “Your password doesn’t matter, but MFA does! Based on our studies, your account is more than 99.9% less likely to be compromised if you use MFA.” This is a Microsoft-attributed finding, not a guarantee for a particular tenant or an independently stated estimate.

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Keep an emergency route into the tenant

Before enabling or changing authentication policies, plan for recovery. Microsoft recommends two cloud-only emergency access accounts and advises that they not be assigned to specific individuals. Its Conditional Access MFA guidance advises excluding emergency access accounts from the user policy scope; it also advises excluding service accounts where applicable. Identify account types and dependencies before deciding on exclusions, and test the recovery process so an accidental lockout does not become a prolonged outage.

Choose security defaults or Conditional Access

Microsoft describes security defaults as a simple, no-license on/off baseline with no customization. Conditional Access supports customized policies and targeting, but requires at least Microsoft Entra ID P1. Microsoft’s Microsoft 365 admin guidance gives Business Premium and E3 as plan examples that include P1, and E5 as an example that includes P2. Verify the licensing in your own tenant: feature requirements differ, and a plan name alone may not establish access to every capability.

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License prerequisite None, according to Microsoft’s comparison At least Microsoft Entra ID P1
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Typical fit Organizations seeking Microsoft’s basic protections with minimal policy design Organizations needing differentiated controls, such as device-compliance conditions or stronger access rules

The fit descriptions are practical interpretations of Microsoft’s documented differences, not a substitute for evaluating your tenant’s requirements.

If you use security defaults

Check for dependencies on older authentication protocols before enabling defaults; Microsoft’s security-defaults guidance specifically warns administrators to do so. The documentation also states that, starting July 1, 2026, new Entra tenants block device-code flow as part of security defaults. Applications or devices that rely on that flow cannot sign in while defaults are enabled. Check current Microsoft documentation and validate dependencies before changing the setting.

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If you move to Conditional Access

Microsoft says security defaults and Conditional Access policies cannot both be enabled at the same time. Treat the change as a migration, not as a simple switch: turn defaults off only as part of the move and recreate their baseline protections in Conditional Access. Microsoft’s documented policy templates include MFA for all users, MFA for administrators, blocking legacy authentication, and MFA for Azure management. Review exclusions, test the policies, and then add custom rules suited to your environment.

Use device context when it helps protect sensitive data

For organizations that need access decisions to account for device state, Conditional Access can require a compliant device before access to sensitive data. Intune evaluates device compliance and provides that signal to Entra ID. Microsoft’s Zero Trust guidance covers cloud-only and hybrid identity environments and includes device enrollment, compliance, identity-risk protections, password protection, self-service password reset, and Intune among its policy areas.

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Do not assume every capability in that guidance comes with the same license. Microsoft lists Microsoft 365 E5, Microsoft 365 E3 with the E5 Security add-on, EMS E5, or Entra ID P2 for some risk-based capabilities, while other features have different requirements. Check licensing for each capability you plan to use.

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Configure email and collaboration protections deliberately

Microsoft says organizations with cloud mailboxes have built-in security features and describes Defender for Office 365 as its primary email and collaboration security solution for Microsoft 365. Its guidance recommends the Standard and Strict filtering levels and suggests using preset security policies to apply them. Choose and review the level appropriate to your environment rather than assuming that built-in protection removes the need for operational oversight.

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Authenticate sending domains

Microsoft advises authenticating outbound sending domains before tuning email policies. SPF authorizes permitted sending services; DKIM lets recipients verify that messages are authorized by the domain and have not changed since signing. Check that legitimate sending services are covered so authentication and filtering decisions are based on correctly configured domains.

Maintain reporting and forwarding controls

For ongoing operations, Microsoft recommends enabling the Outlook Report button and routing user reports for review. Review or prevent external mailbox forwarding rules, and use investigation tools to look for false positives and false negatives. These are ways to improve visibility and response; they do not eliminate phishing.

Use Secure Score as a prioritized checklist

Secure Score brings together Microsoft 365 security recommendations across identities, apps, and devices. Microsoft says it can help report current posture, guide improvements, and compare with benchmarks. Recommendations may receive partial points when a control covers only some users or devices, and the score can recognize some alternate mitigations, including non-Microsoft solutions.

Microsoft explicitly cautions that Secure Score is not an absolute measure of breach likelihood and is not a guarantee against a breach. Its recommendations do not cover every attack surface. Review each recommendation against your threat model and operational needs, prioritize the work that matters, and record accepted risks or alternate controls instead of treating a higher score as proof that the tenant is secure.

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Put the baseline into operation

  1. Inventory dependencies. Identify account types, older authentication protocols, device-code-flow dependencies, existing policies, and the licenses available in the tenant.
  2. Choose the identity baseline. Use security defaults for a simple, non-customizable baseline, or use Conditional Access when you need custom targeting and have at least Entra ID P1.
  3. Protect recovery. Maintain two cloud-only emergency access accounts and test that authorized administrators can use the recovery route.
  4. Apply and verify email controls. Set an appropriate preset policy level, authenticate outbound sending domains, route user reports for review, and review external forwarding.
  5. Add device conditions where justified. Enroll and evaluate devices with the relevant tools, verify feature licensing, and test the effect on access to sensitive data.
  6. Review progress and exceptions monthly. Microsoft recommends running Secure Score monthly. Use it to find and prioritize recommendations, then investigate exceptions and document decisions.

Microsoft’s guidance provides the baseline controls, but the right configuration depends on tenant licensing, account and application dependencies, and the access your organization needs to support.

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