How Microsoft Intune Works: A Complete Guide for IT Admins

If you have ever wondered how a company manages thousands of laptops and phones without physically touching them — the answer is usually Microsoft Intune.

I have been working with Intune for several years now, managing enterprise device fleets across multiple organisations. In this guide, I will walk you through exactly how it works, in plain English, with no unnecessary jargon.

What is Microsoft Intune?

Microsoft Intune is a cloud-based service that lets IT teams manage devices and applications remotely. It is part of the Microsoft 365 family and sits inside the Microsoft Endpoint Manager admin centre.

Think of it as a remote control for every device in your organisation — laptops, phones, tablets, and even desktops. From one place, you can:

• Push software and apps to devices
• Enforce security settings like PIN requirements and encryption
• Wipe a lost or stolen device remotely
• Check which devices are compliant with your company policies
• Block non-compliant devices from accessing company resources like Outlook or SharePoint

How Intune Fits Into the Microsoft Ecosystem

Before we go deeper, it helps to understand where Intune sits alongside the other Microsoft services you might already use.

Entra ID (formerly Azure AD) handles who the user is — their identity, password, and group memberships.

Intune handles what the device is doing — is it encrypted? Does it have the right apps? Is it running an approved OS version?

Conditional Access is the gatekeeper — it checks both identity (Entra ID) and device health (Intune) before allowing access to company data.

How Device Enrolment Works

Enrolment is the process of registering a device with Intune so it can be managed. There are several ways this can happen.

Understanding Compliance Policies

A compliance policy is a set of rules your device must follow to be considered healthy. If a device breaks any of these rules, it is marked Non-Compliant.

Here are common compliance rules IT admins use:

What Happens When a Device is Non-Compliant

This is where Conditional Access comes in. When a device fails a compliance check, Intune marks it as non-compliant. Conditional Access then reads that status and can:

Configuration Profiles: Pushing Settings to Devices

While compliance policies check whether a device meets your standards, configuration profiles actively push settings to the device.

Examples of what you can configure through profiles:

• Wi-Fi settings — push company Wi-Fi credentials so users never have to type a password
• VPN configuration — deploy VPN profiles to all managed laptops automatically
• Email setup — configure Outlook to connect to Exchange Online without user input
• Security settings — disable USB ports, force screen timeout, restrict Bluetooth
• Windows Update rings — control when and how Windows updates are installed

Think of configuration profiles as your silent IT technician — they set up the device exactly how you want it, without the user ever needing to do anything.

App Deployment

Intune can push apps to devices automatically. There are three types of app assignments:

You can target apps to groups of users or groups of devices. For example:

• Push the Cisco VPN client to all devices in the "Remote Workers" group
• Make Power BI Desktop available in Company Portal for anyone in the "Data Team" group
• Uninstall a retired application from all managed devices in one click

The Admin Centre: Where You Manage Everything

All Intune management happens through Microsoft Endpoint Manager Admin Centre at intune.microsoft.com. The main areas you will work in are:

Common Questions I Get From New Admins

Can users see what IT can see on their personal phone?

On personally-owned devices enrolled with the BYOD (Bring Your Own Device) method, Intune can only see the device name, OS version, and whether the device is compliant. It cannot see personal apps, photos, messages, or browsing history.

What happens if a device is stolen?

You can perform a Remote Wipe from the Intune admin centre. For company-owned devices, this wipes everything back to factory settings. For personal BYOD devices, only the work data and apps are removed — personal data stays intact.

Does Intune work without internet?

The device needs internet access to check in with Intune and receive new policies. However, policies that have already been applied continue to work offline.

Summary

Microsoft Intune is a powerful tool that gives IT teams full control over the devices accessing company data — without needing to physically touch each device.

Here is a quick recap of how it all fits together:

• Enrolment — devices register with Intune through Entra ID
• Compliance policies — define the health rules devices must follow
• Configuration profiles — push settings and Wi-Fi, VPN, email configs automatically
• App deployment — install or remove apps silently across your entire device fleet
• Conditional Access — blocks non-compliant devices from accessing Microsoft 365 resources

If you are just getting started with Intune, the best first step is to enrol one test device, create a basic compliance policy, and watch how the whole flow works end to end. Once you see it in action, everything clicks.