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What Microsoft’s New Intune Changes Mean For Your Business in 2026

Microsoft 365 Intune is getting a serious upgrade in 2026, and this time it’s not just another paid add on. Microsoft has announced that several advanced Intune capabilities that used to sit in ...
Monique Googh
December 5, 2025
Microsoft logo inside a modern office building, symbolising enterprise technology and Microsoft 365 updates.

Microsoft 365 Intune is getting a serious upgrade in 2026, and this time it’s not just another paid add on. Microsoft has announced that several advanced Intune capabilities that used to sit in Intune Suite or separate licences will be included in Microsoft 365 E3 and E5.

For many organisations, that means more security and management features included in licences you already own, along with a price rise you will want to understand and plan for.

If you are not sure how this change affects your environment or your licence mix, our team can walk you through the options and help you avoid paying twice for overlapping tools.

Microsoft 365 Intune changes at a glance

Microsoft has announced that the following Intune capabilities will be included in Microsoft 365 plans in 2026:

  • Cloud PKI
  • Endpoint Privilege Management
  • Intune Advanced Analytics
  • Intune Enterprise Application Management
  • Security Copilot
  • Intune Plan 2

These have previously been part of Intune Suite or separate add-ons, which meant extra monthly cost and more complexity when you were trying to build a complete device management and security stack.

At the same time, Microsoft has flagged Microsoft 365 price increases from 2026, with more details to come closer to the date.

In short: more value in E3 and E5, but you need to keep a closer eye on overlap, costs and deployment plans.

Microsoft 365 Intune features being added to E3 and E5

Here is what each of the new Intune capabilities actually gives you in practice.

Cloud PKI

Cloud PKI gives you a cloud hosted public key infrastructure so you do not need to maintain your own certificate services on premises.

That means:

  • Simpler certificate management for Wi Fi, VPN and device authentication
  • Less time spent babysitting aging certificate servers
  • A clearer path away from legacy on premises PKI

If you already pay for Cloud PKI as an add on, this change may create room to reduce cost once Microsoft confirms the final licensing model.

Endpoint Privilege Management

Endpoint Privilege Management lets you control local admin rights at a much more granular level. Instead of giving users full admin or removing it completely, you can:

  • Approve specific elevation requests for certain apps
  • Allow time bound admin elevation
  • Reduce the number of permanent local admins across your fleet

If you are using a third party tool for elevation control and already have Microsoft 365 E5, this could replace that product for cost sensitive customers.

Intune Advanced Analytics

Intune Advanced Analytics is all about better visibility and decision making. It gives you:

  • Deeper health and performance data across devices
  • Better signal on compliance and configuration drift
  • More useful reporting for capacity and lifecycle planning

For larger fleets this can make it easier to roll out changes at scale with confidence instead of guessing based on a few sampled machines.

Intune Enterprise App Management

This is Microsoft’s answer to the pain of third party application management and patching.

The intent is to:

  • Give you a catalogue of common apps
  • Automate packaging and updates
  • Reduce the need for separate tools like Patch My PC in some environments

It is still maturing, but over time this should speed up Intune deployments and make third party patching simpler and more consistent.

Security Copilot

Security Copilot brings Microsoft’s AI driven threat analysis and response into your existing security stack.

For IT and security teams, this means:

  • Faster interpretation of alerts across Microsoft 365 and endpoint security
  • AI assisted incident analysis, summaries and recommended actions
  • Improved ability to respond to threats without deep SOC resources

It is designed to help teams close the skills and capacity gap, not replace traditional tooling. Including it in E3 and E5 drastically increases its reach.

Intune Plan 2

Intune Plan 2 adds several advanced endpoint management capabilities that previously required additional licensing, including:

  • Advanced controls for compliance and configuration
  • Enhanced reporting and analytics
  • Stronger governance features for regulated industries

Bundling this into E3/E5 makes the baseline Intune experience significantly more complete and reduces the gap between core and premium endpoint management.

Microsoft 365 Intune and licence strategy

These Intune changes will have a few ripple effects on licensing.

Some key points to think about:

  • Microsoft 365 E3 vs Business Premium
    For smaller organisations that want to take endpoint management more seriously, Microsoft 365 E3 becomes more attractive once these Intune capabilities are bundled in. You get more of the “enterprise” toolset without bolting on as many extras.
  • Avoiding tool overlap
    If you are paying for Cloud PKI, elevation control or third party patching tools, you will want to reassess once Microsoft confirms commercial details. In some environments the Microsoft stack will be enough, in others you may still need specific third party features.
  • Price rises are coming
    Microsoft has confirmed price increases alongside these additions. Exact Australian pricing will depend on local distributors, but you should expect licence cost to move, not stay flat.

This is the right time to map what you are actually using, check usage against licences and make sure you are not carrying shelfware.

What this means for your environment

For most customers, these changes are good news, but only if you actually use the new features you are paying for.

Some practical next steps:

  • Review your current Intune deployment and see which of these features you can realistically roll out in the next 12 to 18 months
  • Identify any overlapping tools such as Cloud PKI solutions, privilege elevation tools or patching platforms
  • Plan pilots for Endpoint Privilege Management and Enterprise Application Management in lower risk parts of the fleet
  • Work with finance to model the impact of the Microsoft 365 price changes on your 2026 budget

If you already work with us, we will be recommending which features to prioritise in your specific environment and how to line them up with other projects like Windows 11 uplift or security hardening.

How we can help you respond to the new Intune changes

Changes like this are where a bit of planning goes a long way. You do not want to rush into ripping out existing tools, but you also do not want to pay for duplicate capability for years.

We can help you:

  • Review your current Microsoft 365 Intune configuration and licensing
  • Design a staged rollout of the new features that fits your project and change capacity
  • Compare Microsoft’s new capabilities with any third-party tools you already use
  • Communicate changes to your exec team in plain language, including budget impacts

If you would like to talk through what the new Microsoft 365 Intune changes mean for your organisation, get in touch with our team and we can walk you through it.

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