5 Quick Tips for Faster Microsoft 365 Compliance Checks with CIS Benchmarks
If you’ve ever opened the CIS Microsoft 365 Foundations Benchmark and seen nearly 400 pages of dense guidance, you probably thought, “Yeah… I’ll look at this later.”
The thing is, that CIS Benchmark for Microsoft 365 is one of the best free resources you can use to tighten microsoft 365 compliance, prepare for an m365 security audit, and build a solid baseline without guessing. The problem isn’t the content; it’s how to move from a massive PDF to fast, repeatable checks.
In this quick tip guide, we’ll walk through five practical ways to use the CIS benchmark microsoft 365 document more efficiently, so you can check your environment faster, reduce risk, and stop randomly clicking around admin centers hoping you didn’t miss something important.
Tip 1: Start with the Right CIS Benchmark Profiles (Don’t Try to Do Everything)
The CIS Microsoft 365 Foundations Benchmark covers 129 controls and almost every major admin surface in M365: Microsoft 365 admin center, Entra ID (formerly Azure AD), Intune, Exchange, SharePoint, Teams, Fabric, and more. It’s incredibly detailed, but that also makes it overwhelming.
Instead of trying to implement everything, start by choosing the right profile for your organisation.
Use E3/E5 Level 1 and Level 2 the Smart Way
The benchmark breaks recommendations out by license level and security posture:
- E3 Level 1 (L1) – Essential controls for most organisations
- Practical, low-friction
- Clear security benefit
- Designed not to break usability too much
- E3 Level 2 (L2) – Enhanced controls for higher-risk environments
- Defense-in-depth
- May impact user experience or convenience
- E5 Level 1 and Level 2 – Similar idea, but for E5 tenants with more advanced security features.
For faster microsoft 365 compliance checks, do this:
1. Pick your license track first – E3 or E5.
2. Start with Level 1 only. Treat it as your baseline m365 compliance checklist.
3. Only after you’ve stabilised Level 1, start evaluating the Level 2 items that make sense for your risk profile.
To be honest, I’ve seen teams stall for months because they tried to be “perfect” and jumped into every control at once. Level 1 first is usually the most realistic way to show progress quickly and keep stakeholders on side.
Scope Your First Pass by Area, Not Entire Tenant
Even inside Level 1, 129 controls is still a lot.
A quicker approach:
- Pass 1 – Identity & Access
- Pass 2 – Collaboration & Data
- Pass 3 – Device & Endpoint
This way your microsoft 365 security assessment becomes a series of focused mini-audits rather than one huge, painful event.
Tip 2: Prioritise High-Impact Identity Controls First
If you only have time for a subset of the CIS benchmark microsoft 365 guide, spend it on identity and privileged access. Most real-world breaches in Microsoft 365 start there.
The benchmark does a good job of calling out these controls clearly, and they’re some of the fastest to check and understand.
Separate Admin Accounts and Make Them Cloud-Only
One of the very first CIS controls is:
> Ensure administrative accounts are separate and cloud only.
Why this matters:
- Reduces attack surface – Admin accounts don’t use email, Teams, or SharePoint, so they’re not exposed to basic phishing.
- Limits blast radius – In hybrid setups, a cloud-only admin can’t be directly compromised via on-prem AD, and vice versa.
- Clear separation of duties – Users don’t do day-to-day work with privileged accounts.
Fast check for this control:
1. Go to the M365 admin center → Users → Active users.
2. Filter or sort by admin roles.
3. For each admin account, verify:
- It’s cloud-only (not synced from on-prem AD).
- It has a license with no productivity apps (for example, Entra ID P1/P2 only).
This single step alone moves the needle noticeably for microsoft 365 compliance and any upcoming m365 security audit.
Enforce MFA and Strong Authentication for Admins
The CIS benchmark heavily emphasises MFA and, more recently, phishing-resistant MFA for administrators.
Key quick wins:
- Require MFA for all users via Conditional Access (not per-user MFA, which CIS recommends turning off).
- Use authentication strengths in Conditional Access for admin roles:
- For admins, require phishing-resistant methods such as:
- FIDO2 security keys
- Windows Hello for Business
- Certificate-based authentication
Fast way to start:
1. In Entra admin center → Protection → Conditional Access, create a policy that:
- Targets Directory roles → All privileged roles, or at least Global/Privileged roles.
- Grants access only if MFA is required.
2. Add a second policy for those same roles using Authentication strength → Phishing-resistant MFA.
This directly aligns with multiple CIS controls and removes a lot of low-hanging attack paths, while also making your m365 security assessment story much stronger.
Tip 3: Use the CIS Benchmarks as a Structured Audit Script
One of the underestimated strengths of the CIS benchmark microsoft 365 document is that every control comes with:
- A description (what and why)
- Impact (what might break or annoy users)
- Audit steps (how to check the setting)
- Remediation steps (how to fix it)
- Sometimes PowerShell and Graph examples
- References to official Microsoft documentation
Instead of reading it end-to-end, treat it like a guided m365 security audit script.
Turn Recommendations Into Repeatable Checklists
For faster microsoft 365 compliance checks, pull the key parts of each relevant control into your own lightweight checklist or tracker.
For example, for each CIS control you decide to implement, capture:
- Control ID and title
- Profile
- Audit method
- Status
- Evidence location
This effectively becomes your internal microsoft 365 audit preparation workbook. It also makes it way easier to show auditors or security reviewers exactly how you align with the cis microsoft 365 foundations benchmark.
Leverage PowerShell Where CIS Says “Automated”
The benchmark marks each control as:
- Automated – fully checkable by script or tooling
- Manual – needs human validation or review
For the Automated controls, you don’t have to re-invent the wheel:
- Start by using the PowerShell snippets CIS provides (for Entra, Exchange Online, Teams, SharePoint, etc.).
- Save them into a central script or modular functions.
- Run them regularly to confirm you’re still compliant.
This is basically the first step towards microsoft 365 compliance automation without buying anything, and it already speeds up repeat checks dramatically.
Tip 4: Focus Early on Guest Access, Sharing, and Conditional Access
Surprisingly, many tenants have half-decent MFA configured but completely overlook guest access, Teams/SharePoint sharing, and fine-grained conditional access. The CIS benchmark calls all of this out very clearly.
Tightening these areas gives quick, visible risk reduction and is a big plus for any m365 compliance checklist.
Review Guest Users and Public Groups Regularly
The CIS controls include:
- Reviewing guest users at least bi-weekly.
- Ensuring only approved public groups exist.
Fast actions you can take:
- Guest user review
- Remove stale accounts.
- Confirm sponsors/owners for remaining guests.
- Public groups review
This directly supports better microsoft 365 compliance and reduces data exposure from forgotten guest accounts or wide-open groups.
Use Conditional Access Instead of Security Defaults
The benchmark strongly steers you away from relying only on security defaults. Instead, it recommends:
- Disabling security defaults (carefully, in a planned way).
- Replacing them with scoped Conditional Access policies that:
- Require MFA for all users.
- Require stronger MFA for admins.
- Block legacy authentication.
In practice, a basic Conditional Access set that aligns with the cis benchmark microsoft 365 guide might include:
- CA Policy 1 – Require MFA for all users on sign-in.
- CA Policy 2 – Require phishing-resistant MFA for admin roles.
- CA Policy 3 – Block legacy authentication for all accounts.
Those three alone significantly harden your tenant and are very quick wins to show in any m365 security assessment.
Tip 5: Automate Continuous Assessment Instead of Annual Fire Drills
Even if you follow all the previous tips, one-off microsoft 365 compliance checks are not enough. Configuration drift is inevitable: new admins, new apps, new policies, small “temporary” changes that never get reverted.
The CIS documents themselves recognise this; they’re meant to be a living part of a security program, not a one-and-done PDF on your desktop.
Build a Lightweight Continuous-Check Routine
If you’re staying within native tools to start, a realistic pattern could be:
- Monthly
- Rerun key PowerShell checks for admin accounts, MFA, conditional access, and guest accounts.
- Review any major changes to Entra or M365 admin roles.
- Quarterly
- Revisit your chosen Level 1 CIS controls.
- Spot-check Level 2 controls you might be ready to adopt.
Keep your evidence (reports, scripts, screenshots) in one place. That alone makes how to prepare for microsoft 365 security audit a much less stressful question to answer when someone suddenly asks for proof.
Use Automated Microsoft 365 Compliance Tools for CIS Benchmarks
If you want to go further and avoid manually re-running scripts, automated compliance m365 tools can help you continuously track alignment with the cis benchmark microsoft 365.
One example is ConfigCobra, an automated cloud compliance solution designed specifically for Microsoft 365. It can:
- Continuously check your tenant against the 129 CIS Microsoft 365 Foundations Benchmark controls.
- Support both Level 1 (Essential) and Level 2 (Enhanced) profiles.
- Run scheduled assessments (daily, weekly, monthly) so your checks aren’t just once a year.
- Generate audit-ready PDF reports with evidence and remediation guidance.
- Detect configuration drift in real time, which is a huge gap in manual-only approaches.
- Map CIS controls to other standards like NIS2, HIPAA, PCI DSS, ISO/IEC 27001, NIST CSF, which is very handy if you’re juggling multiple regulatory requirements.
For organisations looking at microsoft 365 compliance automation tools or even aiming to become effectively cis certified microsoft 365 aligned in practice, this type of automated m365 compliance assessment is a big accelerator.
You can explore what it does in more detail here: https://configcobra.com/features
The CIS Microsoft 365 Foundations Benchmark is one of the most valuable free resources for tightening microsoft 365 compliance and preparing for any m365 security audit. The challenge isn’t the quality of the guidance; it’s turning a 396-page PDF into something practical and fast.
If you:
1. Start with the right E3/E5 Level 1 profile,
2. Prioritise high-impact identity controls like separate admin accounts and strong MFA,
3. Use the document as a structured audit script instead of a textbook,
4. Tighten guest access, sharing, and Conditional Access, and
5. Move towards continuous, automated checks,
you’ll go from “we downloaded the CIS benchmark microsoft 365 guide once” to a repeatable, defensible m365 security assessment process.
If you’re at the point where manual scripts and spreadsheets are becoming painful, it’s worth looking at automation to keep up. Tools like ConfigCobra can continuously assess your tenant against the CIS benchmark, map results to other frameworks, and give you audit-ready reports without days of prep work. You can learn more at https://configcobra.com/features
Even if you just start with one of the tips above this week—say, separating admin accounts or tightening your Conditional Access—your Microsoft 365 environment will already be in a better place than it was yesterday. And that’s really what good compliance should feel like: small, consistent improvements that actually make you safer, not just more documented.