Microsoft Entra ID Security Baseline: Best Practices 2025

Introduction

A Microsoft Entra ID Security Baseline is the cornerstone of a modern cloud security posture. With identity now the primary attack vector, organisations must adopt controls that are standards-aligned, auditable, and operationally sustainable. Entra ID (formerly Azure Active Directory) governs access to Microsoft 365, Azure, and an expanding ecosystem of SaaS applications; misconfigurations here routinely lead to credential theft, privilege escalation, and data loss.

At LA NET, we implement a security baseline that unifies Microsoft Cloud Adoption Framework (CAF) guidance with CIS Benchmarks, NIST controls, and CISA recommendations. The result is a clear set of prescriptive controls—Multi-Factor Authentication (MFA), Conditional Access (risk-based), Privileged Identity Management (PIM), governance hardening, and break glass account strategy—that reduce exposure without paralysing day-to-day work.

This article is written for technology leaders, security architects, and MSPs who need a repeatable approach that can be rolled out across tenants with minimal friction and maximum assurance. You will learn how to:

• Enforce strong authentication and block legacy protocols that bypass MFA.

• Apply Conditional Access to prioritise risk signals (user and sign-in risk), device compliance, and (optionally) geo/IP context.

• Control privileged access using PIM with just-in-time elevation, approvals, short activation windows, and alerts.

• Harden tenant configuration (group creation, app registrations, user consent, guest governance) to prevent shadow IT and OAuth abuse.

• Establish and protect emergency break glass accounts for operational resilience.

• Implement operational monitoring (Microsoft Sentinel/SIEM) and access reviews to satisfy auditors.

The baseline is pragmatic by design: it delivers immediate risk reduction while providing a roadmap towards Zero Trust—continuous verification across identity, device, network, and data. Where controls may add friction (for example, geo/IP restrictions), we call them out as optional hardening so you can tailor the posture to your user population and regulatory context.

Key Recommendations for Entra ID Security

1. Enforce Strong Authentication

• Require Multi-Factor Authentication (MFA) for all users.

• Block legacy authentication protocols.

• Apply Conditional Access (CA) for adaptive access policies.

💡 Protects against phishing, password spray, and brute-force attacks.
🔗 CIS Microsoft 365 Benchmark | NIST 800-63B

2. Secure Privileged Access with PIM

• Use Just-in-Time (JIT) privileged role activation.

• Require MFA, approvals, and justification for all role activations.

• Enable alerts and logging to monitor privileged role usage.

💡 Reduces standing admin accounts and enforces least privilege.
🔗 CIS Azure Benchmark | NIST 800-53

3. Strengthen Tenant Governance

• Restrict users from creating security groups.

• Restrict application registrations; enforce admin consent workflows.

• Limit guest access; disable self-service purchases.

💡 Prevents shadow IT, rogue apps, and uncontrolled data access.
🔗 CIS Microsoft 365 Benchmark

4. Apply Conditional Access for Risk-Based Defence

• Block high-risk sign-ins and high-risk users.

• Require compliant devices for administrative access.

• Optionally, enforce Geo/IP restrictions for region-bound environments.

💡 Adds defence-in-depth by combining risk signals, device compliance, and location controls.
🔗 CISA Entra Baseline | CIS Azure Benchmark

5. Maintain Emergency Access Accounts

• Keep at least two break-glass Global Administrator accounts.

• Exempt them from CA and MFA.

• Store credentials securely offline and monitor usage via alerts.

💡 Ensures recoverability if Conditional Access or MFA policies misfire.
🔗 CIS Microsoft 365 Benchmark | Microsoft CAF

Business Benefits

• ✅ Reduced attack surface: MFA + blocking legacy auth.

• ✅ Stronger privileged access controls with JIT PIM.

• ✅ Governance maturity aligned with CIS/NIST frameworks.

• ✅ Compliance readiness (ISO 27001, GDPR, NIST CSF).

• ✅ Operational resilience via Microsoft Sentinel monitoring.

Roadmap for Adoption

1. Pilot – Apply Conditional Access to administrators; enable PIM for Global Admins.

2. Rollout – Extend MFA and CA to all users; block legacy authentication.

3. Operationalise – Integrate with Sentinel; review policies quarterly.

4. Continuous Improvement – Update annually in line with CIS/NIST benchmarks.