In this blog post, Managing Certificates on Managed Devices with Intune, we’ll explore how Microsoft Intune helps organizations deploy and manage certificates effectively. Rather than diving into step-by-step technical instructions, this article will focus on the high-level options Intune provides, along with best practices to keep your certificate strategy both secure and efficient.
When it comes to securing corporate devices, digital certificates play a crucial role in authenticating users, encrypting data, and enabling secure communication.
Why Certificates Matter
Certificates are digital credentials that verify identity and secure communications between devices, apps, and services. They are used in scenarios like Wi-Fi authentication, VPN access, email encryption, and TLS for secure web traffic. Without a reliable certificate management process, organizations face risks such as expired certificates causing outages, misconfigured devices, or security gaps from unmanaged endpoints.
This is where Intune, part of Microsoft Endpoint Manager, steps in to simplify certificate lifecycle management across diverse environments.
Intune Certificate Management Options
Intune offers several ways to deliver and maintain certificates on managed devices. The choice depends on your infrastructure, security requirements, and level of automation needed.
1. Simple Certificate Enrollment Protocol (SCEP)
SCEP is one of the most common methods for issuing and renewing certificates automatically. With Intune, you can integrate with a certificate authority (CA) and configure profiles so devices request and install certificates without user intervention. SCEP is scalable and works well for Wi-Fi and VPN scenarios where certificates must be renewed regularly.
2. PKCS Certificates
For environments that need more control, Intune supports PKCS certificates. These can be directly issued from a CA and deployed to devices. PKCS works well for scenarios where certificate templates need to be tightly controlled, but it requires more configuration effort compared to SCEP.
3. Imported Certificates
Intune also supports the import of certificates that are pre-issued. This approach is less dynamic but can be useful in cases where certificates come from external providers or when organizations need to distribute root and intermediate certificates for trust.
4. Derived Credentials
For organizations that use smart cards or PIV/CAC systems, Intune offers derived credentials. These allow users to authenticate securely on mobile devices without needing a physical smart card, improving both user experience and mobility while maintaining compliance.
5. Trusted Root and Intermediate Certificates
Intune allows you to distribute trusted root and intermediate certificates to ensure devices recognize your internal or third-party certificate authorities. This prevents trust issues and supports seamless authentication across your environment.
Best Practices for Managing Certificates with Intune
Simply deploying certificates isn’t enough. To fully leverage Intune’s capabilities, organizations should adopt practices that reduce risk, improve compliance, and simplify operations.
Automate Certificate Lifecycle
Automation is the cornerstone of effective certificate management. Use SCEP or PKCS with Intune to issue and renew certificates automatically, minimizing human error and ensuring certificates don’t expire unexpectedly. Regularly monitor your CA integration to ensure the automation pipeline remains healthy.
Standardize on Certificate Templates
Consistency reduces complexity. Define clear templates for different certificate use cases—Wi-Fi, VPN, or email encryption—and apply them across your device fleet. Standard templates also make it easier to troubleshoot issues and enforce security policies.
Deploy Root Certificates Early
Ensure root and intermediate certificates are deployed before user certificates. Without them, devices may fail to trust issued certificates, leading to connection problems. Root certificate deployment should be one of the first steps in any Intune certificate rollout.
Plan for Hybrid and Multi-Cloud Environments
Many organizations today operate in hybrid setups, combining on-premises Active Directory Certificate Services (ADCS) with Azure services. Intune can bridge these environments, but it’s important to design certificate policies that work across on-premises, cloud, and mobile scenarios. Avoid siloed configurations that complicate user access.
Prioritize Security and Compliance
Certificates are powerful security assets. Protect your certificate authority and restrict access to certificate templates. Regularly audit certificate usage and align with compliance requirements such as ISO 27001 or NIST guidelines. Intune’s reporting and monitoring capabilities can help track deployments and identify gaps.
Educate Users
Even with automation, user awareness is valuable. Provide simple guidance on what certificates do, why they matter, and how to report issues. This helps reduce confusion if connectivity problems arise from certificate-related issues.
The Bigger Picture
Managing certificates on managed devices with Intune is more than a technical task—it’s a strategic step toward securing modern workplaces. Certificates underpin trust, and trust is at the heart of digital transformation. By using Intune’s flexible options—SCEP, PKCS, imported certificates, and derived credentials—organizations can create a seamless, secure environment for users and IT teams alike.
When paired with best practices such as automation, template standardization, and strong compliance measures, Intune transforms certificate management from a manual headache into an automated, resilient process. The result is not only stronger security but also smoother user experiences across desktops, laptops, and mobile devices.
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