Management: Microsoft Intune as the management plane for Windows 365

Overview

Windows 365 supports several management approaches, but the recommended deployment model is to manage Cloud PCs through Microsoft Intune as part of a cloud-native, Zero Trust-aligned operating model.

Windows 365 management is built into Microsoft Intune and the Intune admin center. Cloud PCs can also integrate with existing management tools such as Microsoft Configuration Manager, Group Policy, scripts, and other operational processes where required. However, the recommended deployment model is to use Microsoft Intune as the primary management plane.

Windows 365 supports Microsoft Intune as the primary management authority, with the ability to integrate existing management approaches where required during transition or for specific workloads. There are two approaches:

  • Microsoft Intune management — recommended deployment option.
  • Existing management integration — for transitional, legacy, or specialized requirements.

At a glance: Intune management is the cloud-native default and keeps Cloud PCs in the same management plane as your other Windows endpoints. Existing management integration retains dependencies on on-premises tooling and should be scoped to validated exceptions.

Microsoft Intune is recommended when deploying Windows 365 Cloud PCs. Microsoft Intune provides the primary management plane for configuration, compliance, security baselines, application deployment, reporting, and operational actions.

Cloud PCs are treated like modern Windows endpoints: policy is cloud-delivered, access can be conditioned on device posture, and applications are layered onto the device instead of being baked into a custom image.

Control moves from infrastructure-based tooling to policy-based, cloud-delivered management. Configuration and compliance are enforced through Microsoft Intune policy — Intune supplies device compliance signals, and Microsoft Entra Conditional Access uses those signals to enforce access — rather than relying on legacy on-premises infrastructure.

Why Microsoft recommends Intune management

Cloud-native management removes on-premises management infrastructure while still supporting the Windows applications and controls used in enterprise environments.

  • Cloud-native management — manage Cloud PCs through Microsoft Intune without requiring domain controllers, VPN-dependent management paths, distribution points, or traditional on-premises management infrastructure.
  • Baseline and posture enforcement — use Microsoft Intune security baselines, compliance policies, and Conditional Access to help enforce posture-based access and reduce configuration drift.
  • Visibility and reporting — use Intune and Windows 365 reporting to view Cloud PC state, policy status, app deployment health, and device compliance from a unified admin experience.
  • Consistent configuration — apply policy, apps, and security configuration uniformly across Cloud PCs, regardless of persona or deployment wave.
  • Lower operational overhead — reduce dependency on manual packaging, scripts, Group Policy, and image rebuild cycles as the estate grows.
  • Alignment with cloud management models — Intune management uses the same tooling as other SaaS and Zero Trust workloads, rather than extending on-premises management models into the cloud.

Learn more about Microsoft Intune: What is Microsoft Intune?

Existing management integration: traditional approach

Traditional management uses tools and patterns that were designed primarily for on-premises Windows estates and VDI-like environments. This commonly includes Configuration Manager, Group Policy Objects (GPOs), scripts, custom images, distribution points, and network-dependent deployment workflows. Microsoft Entra-joined Cloud PCs can also be co-managed with Configuration Manager, so organizations can combine Intune-based cloud management with select Configuration Manager workloads during a transition rather than treating the two as mutually exclusive.

These approaches can still be required for some legacy scenarios, especially where application packaging, reporting, operational processes, or compliance controls are tightly coupled to existing tooling. However, they normally increase administrative overhead when applied broadly to Windows 365.

Trade-offs and considerations

  • Manual packaging complexity — app packaging, testing, and deployment workflows often require more hands-on administrator effort.
  • Limited automation — routine tasks can remain dependent on scripts, collections, distribution points, or scheduled administrative processes.
  • Reduced visibility and reporting — reporting can become fragmented across multiple tools, making it harder to understand Cloud PC health and compliance consistently.
  • Scalability challenges — manual work and infrastructure dependencies tend to grow as the Cloud PC estate expands.
  • Image dependency — applications and settings may be baked into custom images, causing every application or configuration change to trigger image maintenance, testing, and republishing.

Learn more about Microsoft Configurations Manager: Microsoft Configurations Manager?

Important

Where Traditional Management may be required, limit it to the affected users or scenarios. Document the workloads involved, the requirement being met, the trade-offs accepted, and the plan to move to the cloud-native model later. Keeping exceptions narrow lets the rest of the deployment retain the benefits of a cloud-native, Zero Trust approach.

Comparison

Capability or requirement Intune management Traditional management
Primary management plane Microsoft Intune Configuration Manager, Group Policy, scripts, and custom workflows
Deployment model Cloud-delivered policies and apps applied over the internet Network-dependent deployment paths, distribution points
Security configuration Intune security baselines, compliance policies, and posture-based access GPOs, scripts, or manually maintained policy sets
Application delivery Intune Win32 apps and Enterprise App Catalog apps (Microsoft 365 E5; separate licensing required on other plans) layered onto Cloud PCs Manual packaging, Configuration Manager apps, scripts, or apps embedded in custom images
Reporting and analytics Unified reporting for Cloud PCs, policies, compliance, and app deployment Varies by solution
Image strategy alignment Works best with Microsoft-provided gallery images and app/policy layering Often reinforces custom or golden image maintenance
User experience More consistent policy and app application across Cloud PCs Dependency on traditional on-premises infrastructure
Operational overhead Lower operational burden as Microsoft and Intune handle more of the management workflow Higher admin effort for packaging, scripts, collections, distribution, and troubleshooting
Recommended use Default option for Windows 365 deployments Use only for validated legacy or specialized requirements

Adoption path

Deploying Cloud PCs with Intune management should start from the cleanest possible cloud-native baseline, then add only the controls, applications, and exceptions required for the target user persona.

  1. Start with Intune as the management authority. Treat Cloud PCs as modern Windows endpoints and use Intune for configuration, compliance, security, applications, and reporting.
  2. Use Microsoft gallery images where possible. Keep the base OS clean and layer applications, configuration, and security policy through Intune rather than embedding changes into custom images.
  3. Apply the Windows 365 security baseline. Use the baseline as a starting point, test it with pilot Cloud PCs, then tailor it only where business requirements demand exceptions.
  4. Deploy applications through Intune. Prefer Intune Win32 apps and Enterprise App Catalog apps (included with Microsoft 365 E5; requires separate licensing on other plans, including E3) for app delivery and updates. Use traditional packaging only when a dependency has been validated.
  5. Use compliance and Conditional Access together. Ensure device posture is part of the access decision so management, identity, and security work together rather than as separate controls.
  6. Standardize by persona. Build a small number of clear Cloud PC personas with consistent policies, apps, and user settings rather than creating one-off exceptions for every deployment.
  7. Keep traditional management as the exception path. If Configuration Manager, GPOs, or scripts are required, define the reason, owner, and exit criteria so the exception doesn't become the default operating model.

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