Delivering Value with Microsoft 365 E3 and E5 Plus Intune

By Nash Pherson, Director of Product, Recast

Organizations evaluating Microsoft 365 licensing often concentrate on pricing, yet the true return is realized through operational impact. Microsoft announced they intend to include key Intune Suite capabilities in Microsoft 365 E3 and E5 plans starting in the third quarter of 2026. For many IT teams, the immediate challenge is determining how to put those bundled capabilities to work in a way that improves everyday operations.

These changes do not introduce a new endpoint management framework. Instead, they strengthen Intune’s position as a centralized platform for managing devices, applications, and user access. Organizations must take stock of where they need to extend this foundation with complementary application and endpoint management tools to unlock the full value of Intune’s capabilities and align them with real operational workflows. 

Application management with reduced administrative overhead

Managing applications at scale remains one of the most resource-intensive responsibilities for IT teams. Ongoing tasks such as maintaining installers, validating detection logic, and coordinating updates consume time and increase the risk of inconsistencies. With Microsoft 365 E5, Intune Enterprise Application Management helps reduce this burden with a managed catalog of commonly deployed third-party applications that Microsoft maintains.

This approach shifts administrators away from manually collecting installers and building deployment logic for widely used software. Supported applications can be deployed directly through Intune, and updates can be applied as new versions become available. For software that is deployed broadly and updated frequently, this can simplify lifecycle management and reduce delays.

Enterprise Application Management is designed to address common application scenarios rather than every possible deployment need. Because of this, most organizations that migrate to Intune still have challenges with application delivery that result in either support issues or delays in remediating security vulnerabilities. Application management solutions close this gap with larger app catalogs, more customization options, and easier admin workflows. The result is an improved digital employee experience and a significant reduction in complexity for IT teams. 

Reporting and analytics that enable earlier intervention

Improving endpoint reliability depends heavily on having consistent and actionable visibility into device behavior. Intune Advanced Analytics, included with Microsoft 365 E3 and E5, extends reporting beyond basic compliance data to include insights into performance trends, battery condition, and user experience indicators.

These insights help IT teams recognize patterns that might otherwise surface only through repeated support incidents. For instance, analytics can reveal groups of devices with slower startup times or higher resource usage, allowing administrators to investigate shared factors such as hardware models or operating system versions. Addressing these trends early can prevent issues from affecting the broader organization.

Advanced Analytics supports both single-device and multi-device queries. Single-device views assist with focused troubleshooting, while multi-device queries make it possible to evaluate performance or compliance across platforms when inventory policies are enabled.

These analytics are intended to provide focused operational insight, which is a great step in the right direction. Many organizations moving from Microsoft Configuration Manager to Intune may still need to seek out other endpoint management solutions with more robust and extensible inventory and reporting.

Integrated remote control within the management platform

Providing remote support to end users becomes more difficult in zero-trust and cloud-managed environments. Intune Remote Help, included with Microsoft 365 E3 and E5, offers an integrated method for IT staff to assist users directly on their devices.

Support sessions are initiated through user-approved access codes and governed by role-based permissions. Because Remote Help is part of the same platform used for device management, support workflows can be streamlined, particularly when extended with endpoint management tools that support interactive and behind-the-scenes workflows.

Cloud PKI as an evolving approach to certificate management

Certificate management has traditionally required dedicated infrastructure and specialized expertise. Microsoft Cloud PKI, available with Microsoft 365 E5, introduces a cloud-based method for issuing and managing certificates through Intune.

By managing certificates alongside device and policy configurations, organizations can support scenarios such as network authentication and secure access without maintaining on-premises certificate servers. This consolidation can simplify parts of the infrastructure while keeping certificate oversight centralized.

Usage patterns for Cloud PKI are still developing, and it may not immediately replace existing certificate solutions in every environment. For many teams, it represents an incremental option for simplifying certificate workflows rather than a comprehensive replacement.

Managing privilege with tighter controls

Applying least-privilege principles without disrupting productivity remains a persistent challenge. Endpoint Privilege Management, included with Microsoft 365 E5, supports this goal by allowing users to request elevated access only when required, rather than granting permanent administrative rights.

IT teams can begin by auditing elevation requests to understand how users interact with privileged tasks. This information helps shape policies that limit disruption while maintaining security controls. Once policies are established, elevation requests can be approved manually or automatically based on defined conditions. Add-on privileged access capabilities can extend Endpoint Privilege Management’s native offerings with support for hybrid environments and remediation for inconsistent connectivity.

Elevation reporting contributes to compliance reviews and offers traceability when investigating security incidents. This approach reduces standing privilege while allowing users to complete necessary tasks without excessive friction.

Converting bundled capabilities into operational gains

There is a clear pattern across application management, analytics, remote support, certificate services, and privilege control: Microsoft is consolidating endpoint management functions within Intune, reducing fragmentation and simplifying oversight for IT teams. However, accelerating adoption and increasing reliable efficiency requires application and endpoint management solutions that fill natural gaps in Intune’s capabilities.

These additions only deliver value when they are deliberately enabled and incorporated into existing workflows. Organizations that align these capabilities with operational objectives can improve efficiency, reduce risk, and create a more consistent experience for end users. 

The expansion of Intune within Microsoft 365 E3 and E5 is about making more effective use of what is already available. With thoughtful adoption, these changes provide a practical foundation for modern endpoint and application management.

Nash Pherson is a Director of Product at Recast where he leads the product roadmap for Right Click Tools by partnering with systems managers to address ConfigMgr and Intune challenges. He previously spent eight years at Microsoft working with U.S. state and local government organizations to maximize their modern workplace investments. Before joining Microsoft, Nash was a Senior Systems Consultant at Now Micro. He was recognized as a Microsoft MVP in Enterprise Client Management/Enterprise Mobility for his community leadership and technical contributions in 2014. A longtime volunteer leader, Nash has served in the Civil Air Patrol since 1996 as a search and rescue incident commander and youth leadership development instructor. Visit Nash on LinkedIn.