Best Practices for Securing Microsoft Intune

Overview

Microsoft's Intune Customer Success team has published a security hardening guide for Intune tenants. The guidance focuses on three core areas: administrative privilege hygiene, authentication security, and change control for sensitive operations.

Least Privilege for Admin Roles

Over-privileged admin accounts are a significant risk in Intune tenants. The guidance recommends:

• Assign built-in Intune roles with the minimum permissions required for each function rather than defaulting to the Global Administrator or Intune Administrator roles
• Use custom roles to scope permissions precisely when built-in roles are broader than needed
• Regularly review role assignments and remove stale or unnecessary delegations
• Separate day-to-day operational roles from emergency access accounts

Phishing-Resistant Authentication and Privileged Access Hygiene

All Intune administrators should be protected by phishing-resistant MFA. The guidance specifically calls out:

• FIDO2 security keys or Windows Hello for Business as preferred authentication methods for admin accounts
• Avoiding SMS and voice call MFA for privileged identities
• Applying Conditional Access policies that enforce compliant devices and phishing-resistant authentication for Intune portal access
• Using Privileged Identity Management (PIM) in Microsoft Entra ID to require just-in-time activation for sensitive Intune roles rather than permanent role assignments

Multi Admin Approval for Sensitive Changes

The guide highlights Multi Admin Approval (MAA) as a control for high-impact Intune operations. When configured:

• Sensitive changes — such as modifying compliance policies, wipe commands, or assignment group membership — require approval from a second administrator before taking effect
• This creates an audit trail and a check against both insider risk and compromised admin accounts

Source

This guidance is based on the official Intune Customer Success blog post published by Microsoft on March 14, 2026.