As organizations increasingly rely on laptops, mobile devices, and cloud‑connected applications, visibility into device health, configuration, and security posture is critical. Performance degradation, outdated configurations, and elevated device risk can negatively affect productivity and increase exposure to security threats.
Microsoft provides an integrated set of services—Microsoft Intune and Microsoft Defender for Endpoint—that support modern device management, evaluate device risk, and help organizations enforce consistent security controls across their environments.
This guide explains how these services work together, the role of Microsoft Configuration Manager, and how built‑in analytics and compliance signals can be used to improve device reliability and security.
The Role of Microsoft Configuration Manager
Microsoft Configuration Manager (formerly System Center Configuration Manager, or SCCM) is an on‑premises management platform used to deploy applications, manage software updates, enforce configuration baselines, and evaluate compliance—primarily for Windows devices.
When Configuration Manager is used together with Microsoft Intune through co‑management, organizations can extend their existing on‑premises management with cloud‑based capabilities. In a co‑managed environment:
- Configuration Manager continues to manage traditional workloads.
- Microsoft Intune adds cloud‑based device management and compliance evaluation.
- Management workloads can be moved gradually from Configuration Manager to Intune.
This approach enables organizations to support both legacy infrastructure and modern cloud‑first device management strategies during transitions or hybrid deployments.
Learn more:
Co-management for Windows devices - Configuration Manager | Microsoft Learn
How Microsoft Defender for Endpoint Contributes to Device Security
Microsoft Defender for Endpoint is a unified endpoint security platform that delivers preventive protection, post‑breach detection, automated investigation, and response. It continuously evaluates device activity and assigns device risk levels based on observed threats and security signals.
Core capabilities include:
- Threat and vulnerability management, which identifies software vulnerabilities and security misconfigurations
- Attack surface reduction capabilities to limit common attack vectors
- Endpoint detection and response (EDR) for alerting, investigation, and forensic analysis
- Automated investigation and remediation to reduce manual response effort
- Threat intelligence derived from Microsoft’s global security telemetry
When Defender for Endpoint is integrated with Microsoft Intune, device risk levels can be used within compliance policies and Conditional Access to restrict access to organizational resources when risk thresholds are exceeded.
What Microsoft Intune Provides
Microsoft Intune is a cloud‑based unified endpoint management (UEM) service that enables organizations to manage devices, protect organizational data, and enforce security requirements across Windows, macOS, iOS, iPadOS, and Android devices.
Core Intune capabilities include:
- Cross‑platform device enrollment and lifecycle management
- Configuration profiles to apply standardized device settings
- Compliance policies to evaluate whether devices meet security requirements
- App protection policies that safeguard organizational data within applications, including on personal (BYOD) devices
- Integration with Microsoft Entra ID Conditional Access for access decisions based on compliance and risk
By integrating Intune with Defender for Endpoint and Conditional Access, organizations can adopt a risk‑based access model that takes real‑time device health and security posture into account.
Learn more:
What is Microsoft Intune - Microsoft Intune | Microsoft Learn
Choosing How to Use Intune and Defender for Endpoint
Microsoft positions these services as complementary:
- Microsoft Intune focuses on device and application management, configuration, and compliance.
- Microsoft Defender for Endpoint focuses on endpoint threat protection, detection, and response.
- Many organizations deploy both to combine centralized management with advanced security capabilities.
Together, they allow device configuration, security monitoring, and access control to operate as a unified system rather than isolated tools.
Microsoft Intune Licensing Overview
Microsoft Intune Plan 1 is included with several Microsoft subscription offerings. For nonprofits and small organizations, Microsoft 365 Business Premium includes Intune Plan 1 by default. Other plans that include Intune Plan 1 (as of March 2025) include:
- Microsoft 365 E3 and E5
- Enterprise Mobility + Security (EMS) E3 and E5
- Microsoft 365 F1 and F3
- Microsoft 365 Government G3 and G5
- Microsoft Intune for Education
Feature availability may vary by license, and organizations should always review the official service descriptions for current inclusions and limitations.
Learn more:
Licenses available for Microsoft Intune - Microsoft Intune | Microsoft Learn
Designing an Effective Device Enrollment Strategy
An effective enrollment strategy establishes consistent management and security controls from the start. Microsoft recommends that organizations:
- Define security and management objectives.
- Select appropriate enrollment methods such as Windows Autopilot, Microsoft Entra ID join, or manual enrollment.
- Apply standardized configuration and security policies.
- Use compliance policies to evaluate device posture.
- Plan for scalability and long‑term device lifecycle management.
- Provide end‑user guidance to support adoption.
Enrollment is the foundation for applying policy, evaluating compliance, and maintaining ongoing visibility into managed devices. [learn.microsoft.com]
Coordinating Intune and Defender During Device Onboarding
Microsoft documents a layered onboarding approach that commonly includes:
- App protection policies
Protect organizational data within supported applications, including on unenrolled BYOD devices. - Device enrollment in Intune
Enables configuration management, compliance assessment, and reporting. - Compliance policies
Define security requirements such as OS version, encryption, password policies, and update status. - Conditional Access
Enforces access decisions based on Intune compliance results and Defender for Endpoint device risk levels. - Configuration profiles
Apply standardized security and operational settings.
This approach helps ensure devices meet baseline security requirements before accessing sensitive organizational resources.
Using Endpoint Analytics to Improve Device Experience
Endpoint Analytics, available in Microsoft Intune, provides insights into device performance, reliability, and user experience. Microsoft positions Endpoint Analytics as an operational analytics tool, not a real‑time threat detection system
With Endpoint Analytics, IT teams can:
- View dashboards showing startup performance, application reliability, and device health
- Compare devices against established performance baselines to identify underperforming endpoints
- Use generated scores and insights to prioritize remediation
- Investigate issues affecting the end‑user experience, such as slow boot times or outdated configurations
These insights help organizations shift from reactive troubleshooting toward proactive device optimization.
Learn more:
Endpoint analytics overview - Microsoft Intune | Microsoft Learn
Summary
By combining Microsoft Intune, Microsoft Defender for Endpoint, and Endpoint Analytics, organizations can manage devices consistently, evaluate device health and risk, and enforce access controls based on real conditions rather than assumptions.
This integrated approach supports modern work by improving visibility, strengthening security posture, and enabling IT teams to make data‑driven decisions that protect users and organizational data.
