10 Critical Entra ID Security Gaps You’re Probably Ignoring Right Now

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Introduction:

Microsoft Entra ID (formerly Azure AD) is the identity backbone for millions of organizations, yet common misconfigurations create massive attack surfaces. Security architect Sean Metcalf’s recent BSides NoVA presentation exposes the most frequently overlooked settings that defenders must urgently address to protect against identity-based attacks.

Learning Objectives:

  • Identify and remediate critical Entra ID misconfigurations that expose your organization to privilege escalation.
  • Implement advanced monitoring and hardening techniques for identity security posture management.
  • Understand the attacker’s perspective on Entra ID exploitation and how to build effective defenses.

You Should Know:

1. Disable Legacy Authentication Protocols

Legacy authentication protocols like POP3, SMTP, and IMAP don’t support multi-factor authentication (MFA), making them prime targets for password spray attacks. Modern authentication should be enforced across all applications.

 PowerShell: Disable legacy authentication protocols
Connect-MgGraph -Scopes "Policy.ReadWrite.Authorization"
$params = @{
displayName = "Block Legacy Auth"
state = "enabled"
conditions = @{
applications = @{
includeApplications = "All"
}
users = @{
includeUsers = "All"
}
clientAppTypes = @(
"exchangeActiveSync"
"other"
)
}
grantControls = @{
operator = "OR"
builtInControls = @(
"block"
)
}
}
New-MgIdentityConditionalAccessPolicy -BodyParameter $params

Step-by-step guide: This PowerShell script using the Microsoft Graph module creates a Conditional Access policy that blocks legacy authentication clients. First, install the Microsoft Graph PowerShell module (Install-Module Microsoft.Graph), connect with appropriate permissions, then execute the policy creation. The policy affects all users and applications, specifically targeting Exchange ActiveSync and “other” client types that represent legacy protocols.

2. Secure Privileged Role Assignments

Entra ID privileged roles like Global Administrator have sweeping access across your tenant. The principle of least privilege should be rigorously applied, with time-bound assignments using Privileged Identity Management (PIM).

 PowerShell: Audit privileged role assignments
Connect-MgGraph -Scopes "RoleManagement.Read.All"
Get-MgRoleManagementDirectoryRoleDefinition | ForEach-Object {
$role = $_
Get-MgRoleManagementDirectoryRoleAssignment -Filter "roleDefinitionId eq '$($role.Id)'" | ForEach-Object {
[bash]@{
RoleName = $role.DisplayName
PrincipalName = (Get-MgUser -UserId $<em>.PrincipalId).DisplayName
AssignmentType = $</em>.AssignmentType
}
}
}

Step-by-step guide: This audit script enumerates all privileged role assignments in your Entra ID tenant. It connects to Microsoft Graph, retrieves all role definitions, then for each role, fetches the assigned principals (users). The output shows role names, assigned users, and assignment type (permanent or eligible). Run this regularly to identify over-privileged accounts.

3. Implement Emergency Access Accounts

Emergency “break glass” accounts are critical for maintaining access when normal authentication methods fail. These accounts must be excluded from MFA, conditional access policies, and have their credentials securely stored.

 PowerShell: Create emergency access account
Connect-MgGraph -Scopes "User.ReadWrite.All", "RoleManagement.ReadWrite.Directory"
$PasswordProfile = @{
Password = "ComplexTempPassword123!"
ForceChangePasswordNextSignIn = $false
}
$EmergencyUser = New-MgUser -DisplayName "EMERGENCY ACCESS - DO NOT DELETE" `
-UserPrincipalName "[email protected]" `
-PasswordProfile $PasswordProfile `
-AccountEnabled $true `
-MailNickname "emergencyaccess"

Assign Global Administrator role
$RoleDefinition = Get-MgRoleManagementDirectoryRoleDefinition -Filter "displayName eq 'Global Administrator'"
$params = @{
"@odata.type" = "microsoft.graph.unifiedRoleAssignment"
principalId = $EmergencyUser.Id
roleDefinitionId = $RoleDefinition.Id
directoryScopeId = "/"
}
New-MgRoleManagementDirectoryRoleAssignment -BodyParameter $params

Step-by-step guide: This creates a dedicated emergency access account with Global Administrator privileges. The account is configured not to require password change on next login to ensure availability. After creation, physically secure the password in a sealed envelope in a safe, and configure monitoring alerts for any usage of this account.

4. Harden Service Principal Configurations

Service principals (enterprise applications) often have excessive permissions that attackers exploit for lateral movement. Regular audits and least privilege assignments are essential for security.

 PowerShell: Audit service principals with high privileges
Connect-MgGraph -Scopes "Application.Read.All", "RoleManagement.Read.All"
Get-MgServicePrincipal -All | Where-Object {
$<em>.AppRoles | Where-Object { $</em>.AllowedMemberTypes -contains "Application" }
} | Select-Object DisplayName, AppId, ServicePrincipalType |
Format-Table -AutoSize

Step-by-step guide: This command identifies service principals that have application permissions (as opposed to delegated permissions), which can be more dangerous as they don’t require user interaction. Review each identified service principal in the Entra ID admin center under “Enterprise applications” and validate whether the assigned permissions are absolutely necessary for its function.

5. Enable Unified Audit Logging

The Unified Audit Log captures crucial security events across Entra ID, Exchange Online, SharePoint, and other services. Without proper logging, detecting and investigating incidents becomes nearly impossible.

 PowerShell: Enable unified audit logging and retrieve critical events
Connect-ExchangeOnline
 Search for specific high-risk activities
Search-UnifiedAuditLog -StartDate (Get-Date).AddDays(-7) -EndDate (Get-Date) `
-Operations "UserLoggedIn", "Add member to role", "Set-Mailbox" `
-ResultSize 5000 | Export-Csv -Path "AuditLog_Review.csv" -NoTypeInformation

Step-by-step guide: This Exchange Online PowerShell command searches the unified audit log for critical security events from the past week, including user logins, role changes, and mailbox modifications. The results are exported to CSV for analysis. Ensure audit logging is enabled in your Microsoft 365 security center, and consider setting up continuous export to a SIEM.

6. Configure Conditional Access Baseline Policies

Conditional Access policies act as gatekeepers for your cloud resources, enforcing security requirements based on user, device, location, and application sensitivity.

 PowerShell: Create Conditional Access policy requiring compliant devices
Connect-MgGraph -Scopes "Policy.ReadWrite.ConditionalAccess"
$params = @{
displayName = "Require Compliant Device for Admin Portals"
state = "enabled"
conditions = @{
applications = @{
includeApplications = @(
"797f4846-ba00-4fd7-ba43-dac1f8f63013"  Microsoft Admin Portals
)
}
users = @{
includeUsers = "All"
}
locations = @{
includeLocations = "All"
excludeLocations = "AllTrusted"
}
}
grantControls = @{
operator = "OR"
builtInControls = @(
"compliantDevice"
"domainJoinedDevice"
)
}
}
New-MgIdentityConditionalAccessPolicy -BodyParameter $params

Step-by-step guide: This policy requires devices to be either Intune compliant or hybrid Azure AD joined when accessing Microsoft admin portals. The policy uses the application ID for Microsoft Admin Portals and applies to all users from all locations except trusted IPs. Test this policy in report-only mode first before enabling.

7. Monitor Risky User Sign-ins and Remediate

Entra ID Identity Protection detects risky sign-ins and vulnerable users based on Microsoft’s threat intelligence. Automated response to these risks can prevent account compromise.

 PowerShell: Get risky users and sign-ins
Connect-MgGraph -Scopes "IdentityRiskyUser.Read.All", "IdentityRiskEvent.Read.All"
 Get high risk users
Get-MgIdentityRiskyUser -Filter "riskLevel eq 'high'" | 
Select-Object UserPrincipalName, RiskLevel, RiskDetail, RiskLastUpdatedDateTime

Get risky sign-ins
Get-MgIdentityRiskyServicePrincipalHistory -All | 
Where-Object {$_.RiskDetail -ne "none"} |
Select-Object ServicePrincipalId, RiskDetail, RiskLevel, Activity

Step-by-step guide: These commands retrieve users and service principals flagged with high risk levels. Review the output to identify compromised accounts requiring password reset or blocking. In the Entra ID portal, you can configure automated responses through Identity Protection policies to require password change or block access based on risk level.

What Undercode Say:

  • Identity has become the primary attack vector, and Entra ID misconfigurations represent low-hanging fruit for attackers.
  • The shift to cloud identity requires a fundamental rethink of traditional perimeter-based security models.
  • Analysis: Metcalf’s presentation highlights that while organizations invest in advanced security tools, they often neglect basic identity hygiene in Entra ID. The most dangerous gaps aren’t esoteric zero-days but mundane misconfigurations in legacy protocol support, privileged access, and monitoring. As identity increasingly becomes the perimeter, these foundational controls determine an organization’s resilience against common attack patterns like BEC, ransomware, and insider threats. The technical guidance provides actionable steps to close these gaps, but cultural change is equally important – identity security must be treated as core infrastructure, not an afterthought.

Prediction:

Within two years, identity-based attacks will surpass all other initial access vectors, with Entra ID misconfigurations enabling 70% of cloud security breaches. Organizations that fail to implement basic Entra ID hardening will experience a 300% increase in business email compromise and ransomware incidents, forcing regulatory bodies to mandate specific identity security controls as compliance requirements. The security industry will respond with automated identity posture management tools that continuously assess and remediate Entra ID configurations.

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