5 Microsoft 365 Security and Compliance Best Practices (2025)

Microsoft 365 is the backbone for many organizations looking to stay competitive and connected in today’s digital-first workplace. However, with its popularity comes the unfortunate realization that it's also a prime target for cyberattacks, compliance challenges, and data breaches. Whether you’re an IT professional, security administrator, or compliance officer, ensuring the safety of your organization’s Microsoft 365 environment has never been more critical. 

We're going to walk you through five key strategies to boost security and compliance in Microsoft 365 while highlighting the tools, automation, and best practices needed to protect your business and its data. By the end, you’ll also discover how Orchestry can supercharge your Microsoft 365 governance efforts. 

Microsoft 365 Security: The 4 Pillars  

Microsoft 365 security can be categorized into four critical pillars. Understanding and leveraging these pillars will help you establish a solid security foundation for your organization:

1. Security and Risk Management  

Reducing risks is crucial for any organization. Microsoft 365 provides tools like Secure Score, which helps assess your system’s security performance and offers actionable recommendations to improve it.  

2. Information Protection  

Microsoft 365 ensures sensitive information stays protected through tools like sensitivity labels and encryption. These tools help manage how data is accessed, shared, and stored.  

3. Threat Protection  

Sophisticated cyberattacks such as phishing, ransomware, and malware are growing. Microsoft Defender for Office 365 offers robust protection by identifying and mitigating threats before they cause harm. Safe Links and Safe Attachments features also shield users from harmful content in emails and files.

4. Identity and Access Management

Identity protection is key to restricting access to unauthorized users. Features like Multi-Factor Authentication (MFA) and Conditional Access policies fortify your organization against unauthorized logins.    

Microsoft 365 Security Features You Need to Know About 

Microsoft 365 is packed with built-in features to enhance security and compliance. Here are the must-knows for every organization:

Exchange Online Protection

• Helps safeguard email communications from spam, malware, and phishing attempts.

Microsoft Defender (Security Center)

• The centralized hub for managing your organization’s security posture.

Microsoft Purview (Compliance Center)

• Dedicated to compliance management, including tracking regulatory requirements and deploying governance policies.

Data Loss Prevention (DLP)

• Prevents sensitive data—like financial records or personal information—from leaking outside of the organization.  

Mobile Device Management (MDM)

• Ensures that all devices accessing Microsoft 365 are secure and compliant.

Privileged Identity Management (PIM

• Manages and monitors access to privileged accounts to prevent misuse or breaches.  

Why Microsoft 365 Security Matters 

With cyberattacks becoming increasingly advanced and data regulations tightening, prioritizing security best practices is no longer optional. A breach isn’t just a technical challenge; it jeopardizes customer trust, damages reputations, and invites hefty regulatory fines. Following best practices within Microsoft 365 ensures your organization is equipped to handle both existing threats and emerging ones. 

For instance, enabling MFA reduces account compromise risks by 99.9%, according to Microsoft. Similarly, adopting a Zero Trust framework—which assumes the worst-case scenario of no implicit trust—ensures every access request is verified thoroughly, preventing unauthorized access.

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Top 5 Microsoft 365 Security and Compliance Best Practices

1. Enable Multi-Factor Authentication (MFA)

Passwords alone aren’t enough to protect your system. Enabling MFA—requiring a second form of verification like a text message or app notification—adds a vital layer of security.  

• Why: Secure accounts from unauthorized access, even if passwords are compromised
• How: Enable MFA through Azure Active Directory within Microsoft 365 Admin Center

2. Adopt a Zero Trust Model  

The Zero Trust security philosophy assumes that every request, whether inside or outside your network, is a potential threat.  

• Why: Prevent malicious actors from gaining access to resources, even within the perimeter
• How: Implement Conditional Access policies and regularly enforce secure access controls like the Principle of Least Privilege (POLP). Limit admin rights to critical tasks only

3. Use Microsoft Defender & Safe Links  

Deploy Microsoft Defender for Office 365 to defend against advanced threats. Safe Links rewrites and scans URLs in real-time to block malicious sites before they load.

• Why: Protect inboxes and users from phishing, malware, and ransomware attacks
• How: Enable Safe Links and Safe Attachments via the Microsoft 365 Security & Compliance Center

4. Apply Sensitivity Labels & DLP Policies

Classify and protect sensitive data using sensitivity labels. Combine this with DLP policies to ensure data doesn’t leave your organization without proper authorization.

• Why: Prevent accidental or malicious exposure of confidential information
• How: Configure sensitivity labels and enforce DLP policies under the Microsoft Purview Compliance Center

5. Monitor & Automate with Orchestry

Even with Microsoft 365’s robust tools, maintaining governance can be challenging. Orchestry enhances security and compliance with simplified automation and monitoring capabilities, such as workspace reviews and governance templates.

• Why: Streamline governance practices while strengthening oversight
• How: Use Orchestry’s features to implement provisioning, track metrics, and enforce compliance policies

Your Microsoft 365 Security Checklist

Here’s a quick checklist to ensure nothing falls through the cracks when securing Microsoft 365: 

Security Configuration

• Enable MFA and configure Conditional Access policies
• Protect administrator accounts with additional safeguards like PIM
• Set secure password policies for all users

Security Monitoring

• Regularly review activity logs and audit trails
• Leverage Secure Score metrics to benchmark and improve your system’s security

Data Protection

• Apply DLP and sensitivity labels to sensitive data
• Encrypt emails and documents to safeguard against unauthorized access

Device Security

• Secure all devices accessing Microsoft 365 using MDM
• Ensure regular updates and patches for devices and applications

Compliance & Awareness  

• Conduct regular security awareness training for all employees
• Periodically review compliance scorecards

Future-proof Your Security with Orchestry

Is Microsoft 365 secure? The answer is yes—but only if you’re taking full advantage of its extensive security features and combining them with best practices and tools like Orchestry.

Orchestry provides a complete governance solution, helping organizations simplify compliance and tighten security with customizable templates, effective provisioning controls, and ongoing analytics.

To learn more about how Orchestry can support your security needs, sign up for a live demo webinar today and experience it firsthand.