How to Use the CIS Benchmark for Microsoft 365 for Microsoft 365

Learn how to use the CIS Benchmark Microsoft 365 guide to harden your tenant, boost microsoft 365 compliance, and prepare for an M365 security audit.

If you’re trying to get serious about microsoft 365 compliance and security, the CIS Benchmark for Microsoft 365 is one of the best places to start. It’s practical, prescriptive, and—maybe most importantly—vendor-neutral.

The Center for Internet Security (CIS) publishes hardened configuration baselines, and their CIS Microsoft 365 Foundations Benchmark gives you a structured way to secure your tenant and prepare for an m365 security audit without guessing. To be honest, many organizations still don’t realize this benchmark exists, or they download the PDF once and never turn it into an actionable plan.

In this guide, we’ll walk step by step through how to obtain, understand, and actually use the cis benchmark microsoft 365 guidance: from choosing the right security level to turning the 60+ recommendations into a practical m365 compliance checklist—and then automating as much of it as possible.

Step 1 – Get Access to the CIS Microsoft 365 Foundations Benchmark

Before you can harden anything, you need the actual benchmark. The transcript you read earlier described the process briefly; here’s the same idea, but broken down clearly.

1.1 Sign up and download the benchmark

The CIS Microsoft 365 Foundations Benchmark is available as a free PDF, but you do need to register with the Center for Internet Security.

High-level process:

1. Go to the Center for Internet Security site and navigate to their Benchmarks section.
2. Search for "Microsoft 365 Foundations" or "CIS Benchmark Microsoft 365".
3. Create or sign in to a CIS WorkBench account.
4. Accept the EULA (license terms).
5. Download the latest "CIS Microsoft 365 Foundations Benchmark" PDF.

You’ll quickly notice CIS offers a lot of benchmarks—Windows, Linux, Exchange Server, SQL Server, VMware, AWS, Azure, Google Cloud, and many others. That’s by design: they provide a consistent security baseline across your stack. For now, focus on the "Microsoft 365 Foundations" entry.

Once the PDF is in your hands, save it somewhere version-controlled or shared (SharePoint, Teams, or your documentation repo). You’ll refer to it constantly if you’re serious about microsoft 365 compliance.

1.2 Understand what the benchmark does (and doesn’t) cover

The CIS Microsoft 365 Foundations Benchmark focuses on configuration—things like:

Account and authentication policies (including MFA)
Administrative roles and access control
Application permissions and OAuth
Data management and retention
Email security settings
Auditing and logging
Storage policies
Mobile device management (MDM) and endpoint controls

This is not a penetration test, and it’s not a complete compliance framework (like ISO 27001 or SOC 2). Instead, it’s a hardening baseline: if you follow these controls, your tenant will be significantly harder to compromise and easier to defend.

Think of it as your foundation. You can then map it to higher-level frameworks later or layer tools on top for automated compliance m365 assessments.

Step 2 – Choose the Right Security Level: Level 1 vs Level 2

One of the first decisions you’ll see in the cis benchmark microsoft 365 document is whether to apply Level 1 or Level 2 controls. This choice affects how aggressive your security configuration will be.

2.1 What Level 1 means

CIS Level 1 is intended for every Microsoft 365 environment:

Minimal or no interruption to normal business workflows
Little or no reduction in functionality
Settings that are broadly safe and low-friction

In practice, Level 1 is ideal if:

You’re just starting with structured microsoft 365 compliance
You have a small IT team and limited change-management capacity
Business units are very sensitive to changes in user experience

For most organizations, Level 1 is a realistic baseline to implement within a few weeks if you manage it well.

2.2 What Level 2 means

CIS Level 2 is for highly secure environments:

Tighter restrictions on access and sharing
More rigorous monitoring and logging
Certain features may be limited or feel "locked down" to users

Level 2 is a better fit when:

You handle regulated or high-risk data (healthcare, finance, critical infrastructure)
You need stronger audit trails for regulatory microsoft 365 audit preparation
Your risk appetite is low and you can tolerate some inconvenience for extra security

You don’t have to choose one forever. Many organizations start with Level 1, stabilize it, and then selectively adopt Level 2 controls in sensitive departments or for privileged accounts.

In my experience, a hybrid strategy works best: Level 1 tenant-wide, Level 2 for administrators and high-risk workloads.

Step 3 – Read the Controls the Right Way (Without Getting Overwhelmed)

The first time you open the PDF, the CIS benchmark microsoft 365 guide can look dense. Each control has several fields, and there are dozens of them. The trick is to understand the structure and then go methodically.

3.1 How each CIS control is structured

Every recommendation in the benchmark follows a consistent pattern. Typically you’ll see:

Title and ID – e.g., "1.1.1 Enable multi-factor authentication for all users"
Profile applicability – whether it applies to Level 1, Level 2, or both
Description – what the setting does
Rationale – why you should do it (risk and benefit)
Audit – how to check if the setting is correctly configured
Remediation – how to configure it step by step
References – links or standard mappings, in some versions

The Audit and Remediation sections are gold when you’re building an m365 security assessment or preparing for an m365 security audit. They tell you exactly how to verify settings and how to fix them.

3.2 Start with the appendix and summary tables

Toward the back of the document, you’ll find an appendix that summarizes all the recommendations in a consolidated table. This is usually where I start when building an m365 compliance checklist because you can:

Scan all controls in one place
See which are Level 1 vs Level 2
Note which ones are "scored" vs "not scored" (i.e., impact secure score or not)

From there, you can export or manually copy the control list into:

A spreadsheet
Planner/Tasks in Microsoft 365
A ticketing system like Jira or ServiceNow

Then you can assign owners, due dates, and track progress.

This simple step turns a static PDF into a living microsoft 365 compliance project instead of just “one more document someone downloaded once.”

Step 4 – Prioritize High-Impact Security Controls First

CIS includes around 60 recommendations for Microsoft 365. You probably won’t implement them all in one go. That’s normal. Focus on the "big rocks"—the controls that massively reduce risk with relatively low disruption.

4.1 Start with multi-factor authentication (MFA)

The benchmark puts MFA front and center, and honestly, that’s absolutely right.

MFA is typically the number one recommendation:

Enable multi-factor authentication for all users
Enforce MFA for administrative roles (Global Admin, Security Admin, etc.)

This single change drastically reduces account takeover risk and is now a baseline expectation in any serious m365 security assessment.

If you haven’t rolled out MFA yet, plan it in phases:

1. Pilot with IT and security teams.
2. Extend to high-risk users (executives, finance, HR).
3. Roll out to all users with clear documentation and support.

Pair MFA rollout with strong user communication so it doesn’t feel like a surprise or a punishment.

4.2 Then move to identities, apps, and data controls

After MFA, target controls that align closely with real-world attack paths and audit expectations:

Account & authentication policies

Tighten password policies, session timeouts, and sign-in risk responses.

Application permissions

Review and restrict third-party app consent and OAuth access; this is often overlooked but very important.

Email security

Configure anti-phishing, anti-spam, and safe links/attachments settings in line with the benchmark.

Auditing & logging

Make sure audit logging is on and properly retained. This directly supports microsoft 365 audit preparation.

Data management & storage policies

Apply retention policies and controls for SharePoint, OneDrive, and Exchange where the benchmark recommends.

Prioritizing these categories helps you quickly improve your security posture while building a nice story for auditors and stakeholders: you’re aligned to a recognized standard (cis microsoft 365 foundations) and tackling the highest-risk areas first.

Step 5 – Turn the Benchmark into a Repeatable Compliance Process

Implementing the CIS benchmark once is helpful. Turning it into an ongoing microsoft 365 compliance practice is where the real value shows up—especially for audits and long-term risk reduction.

5.1 Build an internal M365 compliance checklist and schedule

Use the appendix in the benchmark PDF as your master list and:

1. Create an M365 compliance checklist from the CIS controls.
2. Tag each control as:

Implemented
In progress
Not applicable
Not started

3. Add owners (identity, email, collaboration, security) and target dates.
4. Schedule periodic reviews (at least quarterly) to re-validate key controls.

This is particularly useful when someone asks, "How are we preparing for our next microsoft 365 security audit?" You can point to your checklist, show progress, and reference the CIS standard instead of just saying "we’ve hardened things a bit."

5.2 Automate audits and drift detection where possible

Manually checking 60+ controls quarterly is painful and, frankly, error-prone. This is where microsoft 365 compliance automation starts to pay off.

Automated tools can:

Continuously check your Microsoft 365 tenant against the CIS Benchmark
Alert you when config drift occurs (for example, someone loosens sharing or disables logging)
Generate audit-ready m365 security assessment reports on demand

For example, ConfigCobra is specifically built for automated m365 compliance assessment against the CIS Microsoft 365 Foundations Benchmark. It can:

Automatically assess all 129 CIS Microsoft 365 Foundations controls (Level 1 and Level 2)
Run scheduled assessments (daily, weekly, monthly) with continuous monitoring
Detect configuration drift in near real time
Generate PDF reports with evidence and remediation guidance for auditors
Map CIS controls to other frameworks like NIS2, HIPAA, PCI DSS, ISO/IEC 27001, and NIST CSF
Support custom rules if you need to align with SOC 2, GDPR, or internal policies

Instead of relying only on one-off manual checks, tools like this turn the cis benchmark microsoft 365 guide into a living, automated control system. If you’re curious, you can explore this kind of automation more at https://configcobra.com/compliance

Step 6 – Use CIS Benchmark Alignment to Strengthen Your Audit Story

Finally, don’t underestimate the communication value of aligning to a recognized standard. Auditors, regulators, and even internal leadership like seeing that you’re not just inventing your own rules.

6.1 Map CIS controls to your broader compliance requirements

Once you’ve implemented a good portion of the CIS Microsoft 365 controls, you can map them to other obligations:

ISO 27001 Annex A controls
SOC 2 security criteria
NIST CSF functions
Industry or regional data protection rules

Many microsoft 365 compliance automation tools (including ConfigCobra) already provide mappings from CIS to these frameworks, which saves a lot of manual work. This makes your microsoft 365 audit preparation easier because you’re showing:

Evidence of specific configurations
Proof those configs are continuously monitored
Traceability from controls to higher-level requirements

6.2 Document decisions and exceptions

Not every control will make sense in every environment. That’s okay—as long as you:

Explicitly record which CIS controls you’re not implementing
Document the rationale (business impact, technical limitations, risk acceptance)
Revisit these exceptions at least annually

To be honest, auditors are often more comfortable with a well-documented exception than with a half-configured control that nobody owns. Good documentation around the cis benchmark microsoft 365 decisions shows maturity, not weakness.

The CIS Microsoft 365 Foundations Benchmark is one of the most practical tools you can use to improve microsoft 365 compliance, strengthen your security posture, and simplify your next m365 security audit.

If you follow the steps above—downloading the benchmark, choosing the appropriate security level, understanding the control structure, prioritizing high-impact settings like MFA, and turning everything into a repeatable checklist—you’ll move far beyond ad hoc configuration changes. You’ll have a defensible, standard-based approach to securing your tenant.

From there, the real leverage comes from automation. Instead of manually re-checking dozens of settings every quarter, you can use microsoft 365 compliance automation tools such as ConfigCobra to continuously assess your tenant against the cis benchmark microsoft 365 guide, detect drift, and produce audit-ready reports on demand. That frees your team to focus on strategic improvements rather than repetitive box-ticking.

If you’re ready to go from a static PDF to a living, automated compliance program, explore how ConfigCobra can help at https://configcobra.com/compliance and consider making CIS-aligned, automated assessments a core part of your Microsoft 365 security lifecycle.

Utilizing the CIS Benchmark for Microsoft 365 Effectively