How Defender Intune and Entra ID Secure Microsoft 365 Together

In this blog post How Defender Intune and Entra ID Secure Microsoft 365 Together we will explain how these tools combine to protect your people, devices and business data. Many companies already pay for Microsoft security products, yet a stolen password or infected laptop can still expose sensitive information because the tools were configured separately.

At a high level, Entra ID checks who is requesting access, Intune checks whether their device meets company security requirements, and Defender looks for signs of an active threat. When connected correctly, they share this information before Microsoft 365 decides whether to allow, challenge or block access.

Three tools with three different security jobs

The easiest way to understand the Microsoft security platform is to stop thinking of it as one large product. Each tool answers a different business question.

Microsoft Entra ID checks the person

Microsoft Entra ID, previously called Azure Active Directory, manages user identities and access to Microsoft 365 and other business applications. It checks details such as who the user is, whether they completed multi-factor authentication and whether the sign-in appears unusual.

Entra ID also provides Conditional Access, which is Microsoft’s policy engine for making access decisions. In plain English, it lets you create rules such as, “If someone is accessing financial data from an unmanaged device, require stronger verification or block access.”

Identity security needs careful configuration because one overprivileged or compromised account can provide access to email, files and administration systems. Our guide to Microsoft Entra ID security settings every business should review covers the individual settings in more detail.

Microsoft Intune checks the device

Microsoft Intune manages and secures company computers, phones and tablets. It applies settings, distributes security policies and reports whether each device meets your organisation’s requirements.

For example, Intune can check whether a laptop has disk encryption enabled, a supported operating system, an active firewall and other required protections. It then gives the device a compliant or noncompliant status that Entra ID can use when deciding whether access should be granted.

This is important because a correct password does not make an unsafe laptop trustworthy. For practical guidance, see how to enforce device compliance with Microsoft Intune.

Microsoft Defender checks for active threats

“Microsoft Defender” describes a family of security products. In this context, the main components are Microsoft Defender for Endpoint, which detects suspicious activity on computers and mobile devices, and Microsoft Defender XDR, which brings related alerts together across devices, identities, email and applications.

Defender looks beyond basic configuration. A device might be fully patched and encrypted but still show evidence of malware, ransomware or an attacker attempting to steal credentials. Defender can assign a device risk level, which Intune can use as part of its compliance decision.

How the tools work together during a sign-in

Consider an employee opening SharePoint from a company laptop while working from home. Behind a sign-in that appears simple, the following checks can happen within seconds:

1. Entra ID verifies the identity. It checks the account, authentication method, requested application and other sign-in signals.
2. Intune reports the device’s status. It confirms whether the laptop is managed and meets the company’s security requirements.
3. Defender reports the threat level. It checks whether suspicious behaviour, malicious software or another security concern has made the device risky.
4. Conditional Access applies the rule. Entra ID uses the available signals to allow access, request another verification step or block the connection.
5. The security team receives actionable information. Instead of reviewing disconnected alerts, they can investigate the identity, device and related activity together.

Microsoft’s supported integration allows Defender for Endpoint risk signals to feed into Intune compliance policies, which can then be enforced through Entra Conditional Access. A device identified as risky can be prevented from reaching company resources while investigation and remediation take place.

A practical business scenario

Imagine a 200-person professional services firm. An employee receives a convincing email and enters their Microsoft 365 password into a fake website. The attacker now has a valid username and password.

If the business relies only on passwords and basic antivirus software, the attacker may be able to access email or download files. The IT team might not discover the incident until clients report suspicious messages.

In a connected setup, Entra ID can identify that the sign-in is coming from an unexpected context and require stronger verification. If the attacker cannot satisfy that requirement using an approved method or compliant device, access is denied.

Now assume the employee’s real laptop has also downloaded malicious software. Defender can identify the threat and increase the device’s risk level. Intune can mark it noncompliant, and Entra Conditional Access can temporarily prevent it from accessing Microsoft 365 until the problem is resolved.

The business outcome is not simply “more alerts.” It is a smaller window for an attacker to operate, less data exposed and a clearer investigation for the IT team.

Why integration matters for Essential 8

The Essential Eight is the Australian government’s baseline cybersecurity framework for reducing common attacks. Defender, Intune and Entra ID can support controls including multi-factor authentication, application and operating system patching, application control, user application hardening and restricting administrative privileges. However, buying Microsoft licences does not automatically make a business compliant.

Policies must match your target maturity level, cover the right users and devices, and produce evidence that the controls are operating. Intune reporting, Defender threat information and Entra sign-in records can help create that evidence, but they need regular review.

This is also where integration reduces administration. Instead of maintaining separate spreadsheets and manually checking every laptop, the business can centrally identify devices that have fallen outside policy and take action before they become an audit finding or security incident.

What businesses commonly get wrong

• They configure each product in isolation. Defender generates alerts, Intune manages devices and Entra ID controls access, but no automated response connects them.
• They confuse enrolment with security. A device appearing in Intune does not necessarily mean it is compliant, protected or monitored by Defender.
• They deploy broad blocking rules immediately. Conditional Access policies should first be tested with a pilot group and report-only settings where appropriate, reducing the risk of locking out legitimate users.
• They overlook administrators and emergency access. Privileged accounts require stronger protection, while carefully controlled emergency accounts help prevent a configuration mistake from locking out the entire organisation.
• They never revisit the setup. Employees, devices, applications and business risks change. Security policies that were suitable two years ago may now contain serious gaps.

For a closer look at the access decision itself, read how Conditional Access and Intune work together. Our guide to implementing Zero Trust with Entra ID and Intune also explains how to introduce these checks without making everyday work unnecessarily difficult.

A sensible way to get started

1. Confirm which Microsoft licences and Defender capabilities you already own.
2. Review who has administrative access and how those accounts are protected.
3. Check whether all supported business devices are visible in Intune and Defender.
4. Define what a healthy, compliant device means for your organisation.
5. Connect Defender device risk to Intune compliance and Entra Conditional Access.
6. Test policies with a controlled group before expanding them across the business.

The goal is not to block employees whenever something looks slightly different. It is to make proportionate decisions using the identity, device and threat information Microsoft 365 already collects.

Turn separate security products into one working system

Entra ID controls the front door, Intune checks the condition of the device at that door, and Defender looks for evidence that the device or account is under attack. The strongest protection comes from making those three decisions part of one process.

CloudPro Inc is a Melbourne-based Microsoft Partner and Wiz Security Integrator with more than 20 years of enterprise IT experience. We help organisations across Australia and internationally connect Microsoft 365 security controls in a practical way, without the complexity and overhead of a giant, faceless managed service provider.

If you are unsure whether Defender, Intune and Entra ID are actually working together in your environment, we are happy to review the setup and identify the most important gaps — no strings attached.