Microsoft Intune vs Endpoint Manager: What's the Difference?

Introduction

If you've been researching device management solutions, you've likely come across the terms Intune and Endpoint Manager used almost interchangeably, which can make understanding the intune endpoint manager relationship genuinely confusing. Microsoft has made several branding changes over the years that have blurred the lines between what these products are, what they do, and how they fit together. For small and mid-sized businesses trying to secure and manage their devices without a massive IT department, clarity on this topic matters. This post breaks down exactly what each term means, how the technology works, and what your business should know before making any decisions.

Understanding the Microsoft Endpoint Management Ecosystem

Microsoft Intune is a cloud-based mobile device management (MDM) and mobile application management (MAM) service. It allows IT administrators to control how company devices — including Windows PCs, Macs, iOS devices, and Android devices — are configured, secured, and used. Intune enforces security policies, pushes software updates, manages app deployments, and ensures that only compliant devices can access corporate resources like Microsoft 365 email or SharePoint. It operates entirely through the cloud, which means there is no on-premises infrastructure required to get started.

Microsoft Endpoint Manager, on the other hand, is not a separate standalone product — it is an umbrella brand that Microsoft introduced in 2019 to unify several device management tools under one administrative console. That console, found at endpoint.microsoft.com, brings together Microsoft Intune, Configuration Manager (formerly SCCM), Desktop Analytics, Windows Autopilot, and other related services. So when someone says "Microsoft Endpoint Manager," they are referring to the integrated admin center that houses Intune and its companion tools. As of 2023, Microsoft has largely moved back to branding the overall solution simply as "Microsoft Intune," but the admin portal and the co-management capabilities from the Endpoint Manager era remain fully intact.

How Device Management Actually Works in This Platform

At its core, Intune manages devices through enrollment. When a device is enrolled in Intune — either by the end user or automatically through Azure Active Directory (now called Microsoft Entra ID) — it receives a management profile that allows the Intune service to communicate with it. From that point forward, administrators can push configuration profiles, compliance policies, and app packages directly to the device without needing to be on the same network. This is particularly valuable for businesses with remote employees or distributed teams, since management happens over the internet rather than through a corporate VPN or local server.

Configuration Manager, the other major component that lives inside the Endpoint Manager console, works differently. It was designed for on-premises environments and uses agents installed on Windows devices to manage them at a deeper level — including operating system deployments, software distribution at scale, and hardware inventory. Many larger organizations run both tools simultaneously in a setup called co-management, where devices are enrolled in both Intune and Configuration Manager at the same time. For most SMBs, however, Intune alone is sufficient and far simpler to deploy and maintain. The Endpoint Manager admin center simply provides one place to manage whichever combination of tools your organization uses.

Step-by-Step Guide

1. Confirm Your Licensing: Microsoft Intune is included with Microsoft 365 Business Premium, Enterprise Mobility + Security E3, and several other Microsoft 365 plans. Before setting anything up, verify that your current subscription includes Intune so you are not paying for something you already have access to.
2. Access the Intune Admin Center: Navigate to endpoint.microsoft.com and sign in with your Microsoft 365 global administrator credentials. This portal is where all Intune and Endpoint Manager configuration takes place, and it is the starting point for every task in this guide.
3. Set Up Azure AD / Entra ID Integration: Intune relies on Microsoft Entra ID (formerly Azure Active Directory) for user identity and device registration, so confirm that your users and groups are properly configured there. If you are syncing from an on-premises Active Directory using Entra Connect, make sure that sync is healthy before proceeding with enrollment.
4. Configure Enrollment Settings: In the Intune admin center, go to Devices and then Enrollment to configure how devices will join your management environment. For Windows devices, Windows Autopilot is the most streamlined method; for mobile devices, you can configure Apple Business Manager or Android Enterprise enrollment depending on your device mix.
5. Create and Assign Compliance Policies: Compliance policies define the minimum security requirements a device must meet — such as requiring a PIN, encrypting storage, or running a minimum OS version. Create policies appropriate to each platform (Windows, iOS, Android, macOS) and assign them to the relevant user or device groups in Entra ID.
6. Deploy Configuration Profiles: Configuration profiles push specific settings to devices, such as Wi-Fi credentials, VPN configurations, email account settings, and security baselines. Build profiles for each device type your organization uses and assign them to groups so that devices are automatically configured the moment they enroll.
7. Enable Conditional Access Policies: In the Microsoft Entra admin center, create Conditional Access policies that require devices to be marked compliant in Intune before they can access apps like Microsoft 365. This is the step that ties device compliance to data access, ensuring that an unmanaged or non-compliant device simply cannot reach company resources.

Comparing Your Device Management Options as an SMB

Best Practices

• Start With Security Baselines: Microsoft publishes pre-built security baseline templates inside Intune that apply recommended settings for Windows devices, and deploying these early prevents you from having to build policies from scratch.
• Use Groups Strategically: Assign policies and profiles to Entra ID groups rather than individual users so that new employees automatically receive the correct configuration the moment their account is created and their device enrolls.
• Enable Windows Autopilot for New Devices: Registering new Windows hardware with Autopilot allows devices to self-configure out of the box without IT needing to physically touch them, which saves significant time as your business grows.
• Review Compliance Reports Regularly: The Intune admin center includes built-in reports showing which devices are compliant, non-compliant, or not yet evaluated, and reviewing these at least weekly helps you catch security gaps before they become incidents.
• Test Policies in a Pilot Group First: Before rolling out any new configuration profile or compliance policy to your entire organization, deploy it to a small test group of devices to confirm it behaves as expected and does not disrupt productivity.

Frequently Asked Questions

Is Microsoft Intune the Same Thing as Microsoft Endpoint Manager?

They are closely related but not identical. Microsoft Endpoint Manager was a brand umbrella that Microsoft introduced to group Intune, Configuration Manager, and related tools under a single admin console at endpoint.microsoft.com. Microsoft has since simplified its branding and now refers to the overall solution primarily as Microsoft Intune, but the admin portal still exists and the co-management features that came from the Endpoint Manager era are still fully available. For most SMBs, the practical answer is that you will be working with Intune through the Endpoint Manager admin center, and the naming distinction rarely affects your day-to-day work.

Do SMBs Really Need Intune, or Is It Overkill?

Intune is genuinely well-suited to small and mid-sized businesses, especially those using Microsoft 365, because it is included in many existing plans at no additional cost. The ability to enforce device encryption, require PINs, wipe a lost device remotely, and block non-compliant devices from accessing email are all capabilities that matter even for a 20-person company. Cyber threats do not scale down for smaller organizations, and unmanaged devices are one of the most common entry points for breaches. If your team uses company-owned or personal devices to access business data, Intune provides a practical and affordable layer of protection.

What Happens to a Device When It Is Enrolled in Intune?

When a device enrolls, it receives a management profile that allows Intune to apply policies, push apps, and check compliance status. On personal devices enrolled through the bring-your-own-device (BYOD) model, Intune uses mobile application management to control only the corporate apps and data, leaving personal photos, messages, and apps completely untouched. On company-owned devices, Intune can apply fuller controls including device-level configuration and remote wipe. In both cases, the device continues to function normally for the end user — enrollment is designed to be transparent rather than disruptive.

Can Intune Manage Devices That Are Not Running Windows?

Yes, Intune supports a wide range of platforms including macOS, iOS, iPadOS, Android, and Android Enterprise. This cross-platform capability is one of the reasons it is particularly useful for businesses where employees use a mix of devices. Each platform has its own enrollment method and set of available policies, so the specific controls you can enforce will vary slightly depending on the operating system. Microsoft regularly updates Intune to keep pace with new OS versions from Apple and Google, so support for current platforms is generally reliable.

How Does Intune Interact With Microsoft 365 Apps and Services?

Intune integrates tightly with the broader Microsoft 365 ecosystem, particularly through Conditional Access policies in Microsoft Entra ID. These policies can require that a device be enrolled and compliant in Intune before it is allowed to access services like Exchange Online, SharePoint, Teams, or any other Microsoft 365 application. Intune also integrates with Microsoft Defender for Endpoint to factor device threat levels into compliance evaluations, meaning a device that is flagged by Defender can automatically be marked non-compliant and blocked from accessing data. This layered integration is what makes the intune endpoint manager platform a cohesive security solution rather than just a device configuration tool.

Managing devices across a growing business is complex, and getting the configuration right from the start makes a significant difference in both security posture and day-to-day IT overhead. Always Beyond helps SMBs deploy, configure, and maintain Microsoft Intune so your team can stay productive and your data stays protected without requiring an in-house IT department to figure it all out. To learn how we can simplify your device management, contact Always Beyond today.