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How to Secure Microsoft Intune Administration Using Best Practices

How to Secure Microsoft Intune Administration Using Best Practices

Implement three critical security measures to protect your Microsoft Intune environment: least-privilege RBAC roles, phishing-resistant authentication, and multi-admin approval for sensitive operations.

Emanuel DE ALMEIDAEmanuel DE ALMEIDA
March 18, 2026 18 min 0
hardintune 8 steps 18 min

Why Is Securing Microsoft Intune Administration Critical?

Microsoft Intune administrators wield significant power over your organization's devices, applications, and data. A compromised admin account can lead to widespread device compromise, data theft, or complete organizational disruption. Traditional security approaches often fall short because they rely on perimeter defenses that don't account for the sophisticated attacks targeting cloud administrators today.

What Are the Primary Threats to Intune Administrators?

Modern attackers specifically target administrative accounts through phishing campaigns, token theft, and privilege escalation attacks. They understand that compromising a single Intune administrator can provide access to thousands of corporate devices. The shift to remote work has expanded the attack surface, making traditional network-based protections less effective.

How Do These Security Measures Align with Zero Trust Principles?

The three security measures covered in this tutorial—least-privilege RBAC, phishing-resistant authentication, and multi-admin approval—form the foundation of a Zero Trust approach to Intune administration. Instead of trusting users based on their network location or device, these controls verify every administrative action and limit the blast radius of potential compromises. This approach assumes breach and focuses on minimizing damage rather than preventing all attacks.

Implementation Guide

Full Procedure

01

Audit Current Role Assignments and Remove Excessive Privileges

Start by conducting a comprehensive audit of your current Intune role assignments. Many organizations unknowingly grant excessive privileges that violate the principle of least privilege.

Navigate to the Microsoft Intune admin center at endpoint.microsoft.com and sign in with your administrative account. Go to Tenant administration > Roles > All roles.

Review all current assignments, paying special attention to:

  • Global Administrator assignments (should be minimal)
  • Intune Administrator assignments (often over-assigned)
  • Standing access without time limits
  • Assignments not tied to specific job functions

Document each assignment with the following information:

# Use PowerShell to export current role assignments
Connect-MgGraph -Scopes "RoleManagement.Read.All"
Get-MgRoleManagementDirectoryRoleAssignment | Export-Csv -Path "C:\temp\intune-roles-audit.csv"

Remove excessive privileges: For each over-privileged assignment, click on the role > Assignments > select the user/group > Remove assignment. Document the removal with business justification.

Warning: Never remove your own Global Administrator access without ensuring another admin has equivalent permissions. Always maintain at least two break-glass accounts.

Verification: Run the PowerShell export again and compare the before/after CSV files to confirm privilege reduction.

02

Configure Built-in Roles with Proper Scope Limitations

Microsoft Intune provides several built-in roles designed for specific job functions. Assign these roles instead of broad administrative permissions.

In the Intune admin center, go to Tenant administration > Roles > All roles. Select the appropriate built-in role based on job function:

RoleUse CaseKey Permissions
Help Desk OperatorLevel 1 support staffView devices, restart, sync, retire
Endpoint Security ManagerSecurity team membersManage security baselines, compliance policies
Application ManagerApp deployment teamManage apps, app protection policies
Read Only OperatorAuditors, reporting staffView-only access to all Intune data

For each role assignment:

  1. Click the role name > Assignments > Assign
  2. Add the user or security group
  3. Configure Scope (Groups) to limit which device groups this role can manage
  4. Set Scope (Tags) to further restrict access by organizational unit or region

Example scope configuration:

{
  "role": "Help Desk Operator",
  "assignedTo": "HelpDesk-Level1-Group",
  "scopeGroups": ["Corporate-Devices", "BYOD-Devices"],
  "scopeTags": ["US-East", "US-West"]
}
Pro tip: Use Azure AD security groups for role assignments instead of individual users. This makes management easier and provides better audit trails.

Verification: Test each assignment by having the assigned user log into Intune and confirm they can only access resources within their defined scope.

03

Create Custom Roles for Specific Business Requirements

When built-in roles don't match your organization's needs, create custom roles with precisely the permissions required.

In the Intune admin center, navigate to Tenant administration > Roles > Create > Custom role.

Define the role with these steps:

  1. Basics: Enter a descriptive name like "Regional Device Manager" and description
  2. Permissions: Select only the required permissions. Common custom role scenarios:

Example: Report-Only Security Analyst

{
  "roleName": "Security-Analyst-ReadOnly",
  "permissions": {
    "deviceCompliancePolicy": ["Read"],
    "deviceConfiguration": ["Read"],
    "managedApps": ["Read"],
    "reports": ["Read", "Export"],
    "auditLogs": ["Read"]
  },
  "scopeTags": ["Security-Team"]
}

Example: Limited Device Manager

{
  "roleName": "Regional-Device-Manager",
  "permissions": {
    "managedDevices": ["Read", "Update", "Retire"],
    "deviceCompliancePolicy": ["Read"],
    "deviceConfiguration": ["Read", "Assign"],
    "remoteActions": ["Sync", "Restart"]
  },
  "excludedActions": ["Wipe", "Delete", "FactoryReset"]
}

After creating the custom role:

  1. Go to Assignments tab
  2. Add the appropriate users/groups
  3. Configure scope groups and tags to limit access
  4. Set assignment type to Eligible if using PIM (covered in next step)
Warning: Custom roles with broad permissions can be more dangerous than built-in roles. Always follow the principle of least privilege and regularly review custom role permissions.

Verification: Log in as a user with the custom role and attempt both permitted and restricted actions to confirm the role works as intended.

04

Enable Privileged Identity Management for Time-Bound Access

Implement Privileged Identity Management (PIM) to provide just-in-time access to administrative roles, reducing the attack surface of standing privileges.

Navigate to the Microsoft Entra admin center at entra.microsoft.com and go to Identity > Governance > Privileged Identity Management.

Configure PIM for Intune roles:

  1. Click Microsoft Intune under Azure resources
  2. Select Roles > choose the role to configure (e.g., "Intune Administrator")
  3. Click Settings > Edit

Configure these critical settings:

{
  "activationSettings": {
    "maximumActivationDuration": "PT8H",
    "requireMFA": true,
    "requireJustification": true,
    "requireApproval": true,
    "approvers": ["Security-Admins-Group"]
  },
  "assignmentSettings": {
    "allowPermanentEligibleAssignment": false,
    "maximumEligibleAssignmentDuration": "P365D",
    "requireMFA": true,
    "requireJustification": true
  },
  "notificationSettings": {
    "notifyOnActivation": true,
    "notifyOnAssignment": true,
    "recipients": ["security-team@company.com"]
  }
}

Convert existing permanent assignments to eligible:

  1. Go to Assignments > Eligible assignments
  2. Click Add assignments
  3. Select users who currently have permanent access
  4. Set duration and justification requirements
  5. Remove their permanent assignments after confirming eligible assignments work

Configure emergency access:

# Create break-glass accounts with permanent assignments
# These should be cloud-only accounts with strong passwords
$breakGlassAccount = "breakglass-admin@company.onmicrosoft.com"
# Document these accounts and store credentials securely
Pro tip: Set up PIM alerts to notify security teams of all role activations. This provides real-time visibility into administrative access.

Verification: Test the PIM workflow by having an eligible user request role activation and confirm the approval process works correctly.

05

Configure Phishing-Resistant Authentication with Conditional Access

Implement strong authentication controls that resist phishing attacks by requiring hardware-based authentication methods for administrative access.

In the Microsoft Entra admin center, navigate to Protection > Conditional Access > New policy.

Create a policy specifically for Intune administrators:

Policy Name: "Intune-Admins-Phishing-Resistant-Auth"

Assignments configuration:

{
  "users": {
    "include": [
      "Intune Administrator",
      "Global Administrator",
      "Custom-Intune-Roles"
    ],
    "exclude": [
      "Break-Glass-Accounts"
    ]
  },
  "cloudApps": {
    "include": [
      "Microsoft Intune",
      "Microsoft Intune Enrollment",
      "Microsoft Entra admin center"
    ]
  },
  "conditions": {
    "locations": {
      "include": "Any location",
      "exclude": "Trusted corporate networks"
    },
    "devicePlatforms": {
      "include": "Any device"
    }
  }
}

Access controls configuration:

{
  "grantControls": {
    "operator": "AND",
    "builtInControls": [
      "requireMultiFactorAuthentication",
      "requireCompliantDevice",
      "requireHybridAzureADJoinedDevice"
    ],
    "authenticationStrength": "Phishing-resistant MFA"
  },
  "sessionControls": {
    "signInFrequency": {
      "value": 4,
      "type": "hours"
    },
    "persistentBrowser": {
      "mode": "never"
    }
  }
}

Configure phishing-resistant authentication methods:

  1. Go to Protection > Authentication methods
  2. Enable and configure these methods:
  • FIDO2 security keys: Enable for admin accounts
  • Windows Hello for Business: Require for admin workstations
  • Certificate-based authentication: For smart card users

Disable weak authentication methods:

# PowerShell to disable SMS and voice for admin accounts
Connect-MgGraph -Scopes "Policy.ReadWrite.AuthenticationMethod"
$adminUsers = Get-MgUser -Filter "assignedPlans/any(a:a/servicePlanId eq '12345678-1234-1234-1234-123456789012')"
foreach ($user in $adminUsers) {
    # Disable SMS authentication
    Update-MgUserAuthenticationSmsMethod -UserId $user.Id -Enabled:$false
}
Warning: Test phishing-resistant authentication thoroughly before enforcing. Ensure all admin users have enrolled appropriate authentication methods to prevent lockouts.

Verification: Attempt to sign in as an admin user with weak authentication methods (SMS, app notification) and confirm access is blocked.

06

Deploy Privileged Access Workstations with Security Baselines

Secure the devices that administrators use to access Intune by deploying hardened workstations with Microsoft security baselines.

In the Intune admin center, go to Endpoint security > Security baselines. Select the appropriate baseline for your environment:

  • Microsoft Defender for Endpoint baseline
  • Windows 11 Security Baseline
  • Microsoft Edge baseline

Create a privileged workstation configuration profile:

  1. Select Windows 11 Security Baseline > Create profile
  2. Name: "Privileged-Access-Workstation-Baseline"
  3. Configure these critical settings:
{
  "deviceSecurity": {
    "bitLockerEncryption": "Required",
    "secureBootEnabled": true,
    "tpmRequired": true,
    "windowsDefenderEnabled": true,
    "realTimeProtection": true
  },
  "userRights": {
    "allowLogOnLocally": ["Administrators", "Privileged-Users"],
    "denyLogOnAsService": ["Everyone"],
    "denyNetworkLogOn": ["Guests"]
  },
  "networkSecurity": {
    "windowsFirewallEnabled": true,
    "networkAccessRestricted": true,
    "remoteDesktopDisabled": true
  },
  "applicationControl": {
    "appLockerEnabled": true,
    "allowedApplications": [
      "Microsoft Edge",
      "Microsoft Office",
      "Windows Administrative Tools"
    ]
  }
}

Create a device compliance policy for privileged workstations:

  1. Go to Devices > Compliance policies > Create policy
  2. Platform: Windows 10 and later
  3. Configure these requirements:
{
  "deviceHealth": {
    "requireBitLocker": true,
    "requireSecureBoot": true,
    "requireCodeIntegrity": true,
    "requireHealthAttestation": true
  },
  "deviceProperties": {
    "minimumOSVersion": "10.0.22000",
    "maximumOSVersion": "10.0.99999",
    "requirePasswordType": "alphanumeric",
    "minimumPasswordLength": 14
  },
  "systemSecurity": {
    "requireAntivirusEnabled": true,
    "requireAntiSpywareEnabled": true,
    "requireFirewallEnabled": true
  }
}

Assign policies to privileged user groups:

  1. Create an Azure AD group: "Privileged-Access-Users"
  2. Add all administrative users to this group
  3. Assign both the security baseline and compliance policy to this group
Pro tip: Use Windows Autopilot to automatically provision privileged workstations with these security configurations, ensuring consistent deployment.

Verification: Check device compliance status in Devices > Monitor > Device compliance and confirm all privileged workstations meet the policy requirements.

07

Enable Multi-Admin Approval for Sensitive Operations

Implement multi-admin approval to prevent single-person risk for critical operations like device wipes, role assignments, and script deployments.

In the Intune admin center, navigate to Tenant administration > Multi-admin approval. Click Enable multi-admin approval.

Configure approval workflows for these critical operations:

{
  "approvalWorkflows": [
    {
      "operation": "Role management",
      "description": "Creating, modifying, or deleting Intune roles",
      "enabled": true,
      "requiredApprovers": 1,
      "approverGroups": ["Security-Admins", "IT-Directors"]
    },
    {
      "operation": "Device wipe",
      "description": "Factory reset or selective wipe operations",
      "enabled": true,
      "requiredApprovers": 1,
      "approverGroups": ["Device-Managers", "Security-Team"]
    },
    {
      "operation": "Script deployment",
      "description": "PowerShell script deployment to devices",
      "enabled": true,
      "requiredApprovers": 2,
      "approverGroups": ["Security-Admins", "Change-Advisory-Board"]
    },
    {
      "operation": "Compliance policy changes",
      "description": "Modifications to device compliance policies",
      "enabled": true,
      "requiredApprovers": 1,
      "approverGroups": ["Compliance-Officers", "Security-Team"]
    }
  ]
}

Configure approver settings:

  1. Click Settings in the multi-admin approval section
  2. Set approval timeout: 24 hours for standard operations, 4 hours for urgent requests
  3. Enable email notifications for pending approvals
  4. Configure emergency override procedures

Set up emergency access procedures:

{
  "emergencyAccess": {
    "breakGlassAccounts": [
      "emergency-admin-1@company.onmicrosoft.com",
      "emergency-admin-2@company.onmicrosoft.com"
    ],
    "emergencyBypassEnabled": true,
    "postEmergencyReviewRequired": true,
    "emergencyJustificationRequired": true,
    "auditLogRetention": "P2555D"
  }
}

Test the approval workflow:

  1. As a regular admin, attempt to wipe a test device
  2. Verify the operation is blocked and approval request is sent
  3. As an approver, review and approve the request
  4. Confirm the original operation can now proceed
Warning: Ensure you have sufficient approvers available during business hours and establish clear emergency procedures for after-hours critical operations.

Verification: Monitor approval requests in Tenant administration > Multi-admin approval > Pending requests and review the audit logs for all approved operations.

08

Configure Advanced Monitoring and Alerting

Set up comprehensive monitoring to detect suspicious administrative activities and potential security breaches in your Intune environment.

Configure Microsoft Defender XDR integration:

  1. In the Microsoft Defender portal (security.microsoft.com), go to Settings > Microsoft 365 Defender
  2. Enable Microsoft Intune data connector
  3. Configure these alert rules:
{
  "alertRules": [
    {
      "name": "Suspicious Admin Activity",
      "conditions": [
        "Multiple failed admin sign-ins",
        "Admin access from unusual location",
        "Bulk device operations",
        "Role assignment changes"
      ],
      "severity": "High",
      "actions": ["Email security team", "Create incident"]
    },
    {
      "name": "Privileged Role Activation",
      "conditions": [
        "PIM role activation outside business hours",
        "Emergency access account usage",
        "Multiple role activations by same user"
      ],
      "severity": "Medium",
      "actions": ["Log to SIEM", "Notify manager"]
    }
  ]
}

Set up Intune audit log monitoring:

  1. In Intune admin center, go to Tenant administration > Audit logs
  2. Configure log retention and export settings
  3. Set up automated monitoring for these events:
# PowerShell script to monitor critical Intune events
$criticalEvents = @(
    "Role assignment created",
    "Role assignment deleted", 
    "Device wiped",
    "Compliance policy modified",
    "Security baseline changed",
    "Conditional access policy modified"
)

# Query audit logs for critical events
Connect-MgGraph -Scopes "AuditLog.Read.All"
$auditLogs = Get-MgAuditLogDirectoryAudit -Filter "activityDisplayName in ('$($criticalEvents -join "','")') and activityDateTime ge $((Get-Date).AddHours(-24).ToString('yyyy-MM-ddTHH:mm:ssZ'))"

# Send alerts for any critical events
foreach ($log in $auditLogs) {
    Send-MailMessage -To "security-team@company.com" -Subject "Critical Intune Event Detected" -Body "Event: $($log.ActivityDisplayName) by $($log.InitiatedBy.User.UserPrincipalName)"
}

Configure sign-in risk monitoring:

  1. In Microsoft Entra admin center, go to Protection > Identity Protection
  2. Configure user risk policy for admin accounts:
{
  "userRiskPolicy": {
    "assignments": {
      "users": ["All admin roles"],
      "conditions": {
        "userRisk": ["High", "Medium"]
      }
    },
    "controls": {
      "access": "Block",
      "requirePasswordChange": true
    }
  },
  "signInRiskPolicy": {
    "assignments": {
      "users": ["All admin roles"],
      "conditions": {
        "signInRisk": ["High"]
      }
    },
    "controls": {
      "access": "Block"
    }
  }
}

Set up SIEM integration:

# Export Intune logs to Azure Sentinel/SIEM
$workspaceId = "your-log-analytics-workspace-id"
$workspaceKey = "your-workspace-key"

# Configure data connector for Intune logs
New-AzSentinelDataConnector -ResourceGroupName "security-rg" -WorkspaceName "security-workspace" -Kind "MicrosoftThreatIntelligence"
Pro tip: Create custom workbooks in Azure Monitor to visualize Intune administrative activities and identify patterns that might indicate compromise.

Verification: Generate test events (like role assignments) and confirm they appear in your monitoring dashboards and trigger appropriate alerts.

Frequently Asked Questions

What is the difference between Microsoft Entra ID P1 and P2 licenses for Intune security?+
Microsoft Entra ID P2 is required for advanced security features like Privileged Identity Management (PIM), Identity Protection with risk-based policies, and advanced Conditional Access features like authentication strength policies. P1 provides basic Conditional Access and MFA, but lacks the just-in-time access controls and risk detection capabilities essential for securing privileged Intune administrators. For comprehensive Intune security, P2 licensing is strongly recommended for all administrative accounts.
How does multi-admin approval work with emergency situations in Microsoft Intune?+
Multi-admin approval includes emergency override capabilities for critical situations. Break-glass accounts can bypass approval requirements, but all emergency actions are logged and require post-incident review. Organizations should configure emergency procedures with clear escalation paths, document break-glass account usage, and implement automated alerts when emergency overrides are used. The system allows configuring different approval timeouts for urgent versus standard requests, typically 4 hours for emergencies versus 24 hours for routine operations.
Can phishing-resistant authentication methods be enforced for all Intune administrators?+
Yes, phishing-resistant authentication can be enforced through Conditional Access policies and authentication strength requirements. Supported methods include FIDO2 security keys, Windows Hello for Business, and certificate-based authentication. However, organizations must ensure all administrators have enrolled appropriate authentication methods before enforcement to prevent lockouts. The policy should exclude break-glass accounts and provide fallback procedures. Testing in report-only mode is recommended before full enforcement.
What are the most common RBAC mistakes when securing Microsoft Intune?+
Common RBAC mistakes include over-assigning Global Administrator roles, creating custom roles with excessive permissions, not using scope tags to limit access by organizational boundaries, and failing to regularly audit role assignments. Many organizations also neglect to implement time-bound access through PIM, leaving standing privileges that increase attack surface. Another frequent error is not testing role assignments thoroughly, leading to either excessive permissions or users unable to perform required tasks.
How should organizations monitor and respond to suspicious Intune administrative activity?+
Organizations should implement comprehensive monitoring using Microsoft Defender XDR integration, Entra ID audit logs, and Intune-specific audit trails. Key indicators include multiple failed admin sign-ins, access from unusual locations, bulk device operations, unexpected role changes, and off-hours privileged access. Response procedures should include automated alerting to security teams, incident creation in SIEM systems, and immediate investigation protocols. Integration with Azure Sentinel or other SIEM platforms enables correlation with broader security events and automated response workflows.
Emanuel DE ALMEIDA
Written by

Emanuel DE ALMEIDA

Microsoft MCSA-certified Cloud Architect | Fortinet-focused. I modernize cloud, hybrid & on-prem infrastructure for reliability, security, performance and cost control - sharing field-tested ops & troubleshooting.

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