Microsoft’s New Intune Licensing Changes: What You Need to Know

At the end of 2025, Microsoft announced a series of licensing changes affecting the Intune Suite bundle. What made the timing interesting is that these updates didn’t appear at Ignite in November—where they typically would have—but were released quietly a few weeks later. Why Microsoft chose to do this isn’t entirely clear, but it’s hard not to see a connection to the recent shift of Security Copilot being included in all Microsoft 365 E5 licenses. It feels like part of a broader realignment of how Microsoft packages its management and security tools.

What has changed?

Microsoft 365 E3 and E5 prices are increasing, but key Intune features that were previously locked behind Intune Plan 2 or the Intune Suite are now included directly in both plans.

License	Price
Microsoft 365 E3	$36 → $39 per user/month
Microsoft 365 E5	$57 → $60 per user/month

With that additional $3 per user, organizations get access to features that once required separate add‑on licensing. This includes tools like Intune Tunnel for MAM, specialty device management, firmware‑over‑the‑air updates, Remote Help, and Advanced Analytics. E5 customers get even more with Endpoint Privilege Management, Enterprise Application Management, Cloud PKI, and Security Copilot functionality.

Below is a comparison table that shows all of the features now included in both E3 and E5 licensing.

Feature	Microsoft 365 E3	Microsoft 365 E5
Intune Tunnel for MAM	Yes
Management of Specialty devices	Yes
Firmware-over-the-air (FOTA) updates	Yes
Remote Help	Yes
Advanced Analytics	Yes
Endpoint Privilege Management	—	Yes
Enterprise Application Management	—	Yes
Cloud PKI	—	Yes
Security Copilot	—	Yes

Beyond the Intune‑specific features, Microsoft is also adding several new capabilities to the E3 tier that weren’t previously part of the Intune Suite.

Feature	Microsoft 365 E3	Microsoft 365 E5
Quick Machine Recovery (QMR)	Yes
Cloud rebuild for Windows 11	Yes
Point-in-time restore for desktop	Yes
Post-quantum security APIs	Yes
Autopatch update readiness	Yes

Understanding the Bigger Picture

To fully evaluate whether these changes benefit your organization, it helps to compare what’s included in Intune Plan 1, Intune Plan 2, and the Intune Suite. Many of the features now showing up in E3 and E5 were once exclusive to Plan 2 or the Suite, which changes the cost‑benefit analysis for anyone currently paying for those add‑ons.

Below is the current lineup of Intune features with the Intune Plans and Intune suite.

Plan	Price	Notes
Intune Plan 1	$8.00 user/month	Included with Microsoft 365 E3
Intune Plan 2	$4.00 user/month	Add-on that includes the features mentioned in the table above, included in the Intune Suite
Intune Suite	$10.00 user/month	Add-on, includes all Intune features including Intune Plan 2

Feature	Intune Plan 1	Intune Plan 2	Intune Suite
Core Capabilities	Yes
Intune Tunnel for MAM	—	Yes
Management of Specialty devices	—	Yes
Firmware-over-the-air (FOTA) updates	—	Yes
Remote Help	—	—	Yes
Endpoint Privilege Management	—	—	Yes
Advanced Analytics	—	—	Yes
Enterprise Application Management	—	—	Yes
Cloud PKI	—	—	Yes

Now that many of these capabilities are included directly in E3 and E5, the value proposition shifts significantly. For some organizations, this may eliminate the need for additional Intune licensing entirely.

Final Thoughts

These licensing changes will be great news for some and less exciting for others. It largely depends on which Intune features your organization actually uses today—and how many of them you were paying extra for. But one thing is clear: Microsoft is streamlining its licensing model and bringing more advanced features into the mainstream plans.

I’d love to hear what you think.
Are these changes helpful for your environment?
Drop a comment below and share your thoughts!

For more information on these changes, see

Microsoft 365 adds advanced Microsoft Intune solutions at scale - Microsoft Intune Blog