Complete Guide to Microsoft 365 CIS Compliance

Microsoft 365 does ship with some security defaults, but they’re intentionally generic. They’re okay for micro‑organizations with no IT support, but they’re not enough for regulated businesses or anyone heading into a formal m365 security assessment.

Moving from “secure by default” to “secure by design” usually means:

• Turning off blanket Security Defaults so you can use Conditional Access and fine‑grained controls
• Enforcing multi-factor authentication (MFA) in a robust way
• Restricting where and how people can sign in
• Tuning sharing, session controls, and mobile access

These are essentially the same categories you’ll see in the CIS Microsoft 365 Foundations guidance—they just speak more plainly here.

Auditors often don’t ask, “Did you tick box 56 of the CIS benchmark?” Instead, they ask:

• How do you enforce MFA across your tenant?
• How do you control access from risky locations or devices?
• How do you govern third‑party apps and data sharing?
• Do you have a repeatable microsoft 365 audit preparation process?

If you can say, “We align to the cis microsoft 365 foundations benchmark and we run an automated M365 compliance assessment against all 129 controls on a schedule,” your life becomes dramatically easier.

That’s why there’s so much interest now in cis certified microsoft 365 style postures and in tools that automate these checks. You’re not just “secure” in theory—you can show proof on demand.

This sounds backwards at first: you actually start by turning off Security Defaults.

Security Defaults provide a very coarse, one‑size‑fits‑all security posture. To implement the more granular CIS Benchmark Microsoft 365 recommendations, you need Conditional Access policies instead.

High‑level process:

1. Go to the Microsoft Entra admin center → Identity → Properties.
2. Scroll down to Security defaults.
3. Set it to Disable, and specify that your organization will use Conditional Access.

Why this matters for compliance:

• CIS strongly favors policy‑based access control
• Auditors like to see documented, explicit policies rather than opaque defaults

Just be careful: don’t disable Security Defaults without having a plan for replacement policies.

Next, enforce MFA through Conditional Access.

A clean way is to start from Microsoft’s template:

1. In Entra admin → Identity → Protection → Conditional Access → Policies → New policy from template.
2. Choose something like “Require multi-factor authentication for all users.”
3. Give it a clear name (for example, `CA01 – Require MFA for all users`).
4. On an existing tenant, set the policy state to Report-only first.

Why report-only? Because turning MFA on instantly for every user can cause lockouts and panic if you haven’t communicated, trained, or validated devices.

Later, once you’re sure:

• Confirm your authentication methods are configured (see below).
• Switch the policy to On.

CIS & audit tie‑in:

• MFA is one of the most visible controls in any m365 security audit.
• The CIS Benchmark explicitly calls for MFA for all privileged and standard accounts.

Not all MFA is equal anymore. SMS and phone call MFA are increasingly attacked (SIM‑swapping, call interception, etc.).

In Entra admin → Identity → Authentication methods:

• Enable Microsoft Authenticator for all users.
• Enable FIDO2 security keys for hardware-based MFA (for example, YubiKeys).
• Prefer to disable or at least minimize SMS/voice call MFA.

This lines up with CIS guidance to use phishing‑resistant or stronger MFA mechanisms where possible. In my experience, auditors like seeing FIDO2 options even if adoption is still partial—it shows a forward‑looking security stance.

By default, anyone on the planet can attempt sign‑in to your tenant. For many organizations, that’s unnecessary risk.

You can implement geographic restrictions with Conditional Access Named Locations:

1. In Entra admin → Conditional Access → Named locations.
2. Create a location such as `Approved Countries` (e.g., United Kingdom, or UK + EU, etc.).
3. Create a new Conditional Access policy (e.g., `CA02 – Block access from non-approved countries`).
4. Assign to All users, but exclude a break-glass admin account.
5. Target All cloud apps.
6. Under Conditions → Locations:

• Include Any location.
• Exclude your Approved Countries location.

7. Under Access controls → Grant/Block, choose Block access.

Result: Login attempts from outside your allowed regions are blocked.

This kind of control is not only good practice, it’s a common item on an m365 security assessment checklist for organizations with location‑bound operations.

Real life: your CEO goes to Greece with their laptop, and suddenly your “block non‑UK logins” rule locks them out.

To avoid this while staying secure, you can use device filters in Conditional Access:

• Still block non‑approved countries by default.
• Add a filter to exclude Intune‑managed, compliant devices from that block rule.

In the CA policy:

1. Under Conditions → Filter for devices, configure:

• Exclude devices where property `isCompliant` equals `true`.

This effectively says: “We block sign‑ins from outside approved countries unless you’re on a managed, compliant device.”

It’s a nice example of taking a blunt control and tuning it into something usable for a modern hybrid workforce, while still satisfying CIS-style requirements for managed device access.

If your business only uses Windows and maybe macOS, why allow sign‑ins from Linux desktops, Windows Phone, or random platforms you don’t support?

You can tighten this via another Conditional Access policy:

1. Create `CA03 – Block unapproved device platforms`.
2. Assign to All users.
3. Target All cloud apps.
4. Under Conditions → Device platforms:

• Select platforms you want to block (e.g., Windows Phone, Linux, maybe others you don’t support).

5. Under Access controls → Grant/Block, choose Block access.

This is relatively simple, but it aligns very well with CIS recommendations to control access by device type and to only allow supported, managed platforms.

Persistent browser sessions keep users signed in even when they close their browser tab. Convenient, but risky—especially on shared or personal devices.

To reduce that risk:

1. Create `CA04 – Disable persistent browser sessions`.
2. Assign to All users, All cloud apps.
3. Under Conditions → Client apps, target Browser.
4. Under Session controls, set Persistent browser session to Never persistent.

This forces re‑authentication more frequently and mitigates scenarios where someone closes a browser and assumes they’re logged out—but they aren’t.

From a microsoft 365 compliance perspective, this kind of control is often cited as evidence of reasonable session management and reduces unauthorized access via shared machines.

Most staff want work email and Teams on their personal smartphones, which is understandable and, honestly, normal now. But unmanaged mobile access is a classic data leakage risk.

The approach:

• Use Intune App Protection Policies for Office mobile apps (no full device enrollment required).
• Enforce those policies via Conditional Access.

High‑level Conditional Access configuration:

1. Create `CA05 – Require app protection policy for mobile`.
2. Assign to All users.
3. Under Cloud apps, select Office 365.
4. Under Conditions → Device platforms, select Android and iOS.
5. Under Client apps, target Browser and Mobile apps and desktop clients.
6. Under Access controls → Grant, Grant access but require app protection policy.

This is the essence of modern, app‑centric mobile security and maps well to CIS controls around protecting data on mobile endpoints without over‑controlling personal devices.

Newer Microsoft 365 tenants often have legacy authentication disabled by default, but it’s still worth enforcing with a Conditional Access policy.

You can use Microsoft’s template:

1. In Conditional Access → New policy from template.
2. Choose Block legacy authentication.
3. Give it a clear name such as `CA06 – Block legacy authentication`.
4. Assign to All users.
5. Turn the policy On.

This is practically a non‑negotiable control for any serious m365 security audit. CIS explicitly calls out disabling weaker legacy protocols that don’t support modern security features like MFA.

Joining devices to Entra ID (Azure AD) is a powerful action. If attackers can do it easily, they can onboard rogue hardware into your environment.

Create a Conditional Access policy that requires MFA for device registration:

1. Create `CA07 – Require MFA to join to Entra ID`.
2. Assign to All users.
3. Under Target resources, pick User actions → Register or join devices.
4. Under Access controls → Grant, Grant access but require MFA.

This is a relatively small step that dramatically reduces the risk of unauthorized devices getting a foothold.

In Entra admin → Identity → Users → User settings, you’ll find:

• Restrict non-admin users from creating tenants

Set this to Yes/On so that only admins can create new Azure AD/Microsoft 365 tenants.

Why this matters:

• Prevents shadow IT “side tenants” where governance, logging, and compliance controls don’t exist
• Supports centralized management, which auditors usually ask about during microsoft 365 audit preparation

In the same User settings area, enable:

• Restrict access to Microsoft Entra admin center

This ensures that only admin roles can access the admin portal, which:

• Reduces the risk of curious or malicious standard users poking around
• Demonstrates good role‑based access control, a common m365 security assessment checkpoint

Third‑party applications can request access to your Microsoft 365 data via OAuth. By default, any user can consent to many of these apps, which is rarely ideal.

In Entra admin → Enterprise applications → Consent and permissions:

• Avoid “Allow user consent for apps – All users can consent for any app”.
• Prefer one of these:
• Allow user consent for apps from verified publishers (safer, but still some risk), or
• Do not allow user consent; require administrator approval for all apps (strictest and generally best for compliance‑sensitive orgs).

Also disable group owner consent if still available:

• Set Group owner consent to Do not allow.

This aligns perfectly with CIS guidance on app governance and is often a direct answer to the audit question: “How do you control third‑party access to Microsoft 365 data?”

Finally, some crucial but often overlooked SharePoint and OneDrive settings.

In the SharePoint admin center → Policies → Sharing:

1. Reduce anonymous sharing:

• Instead of “Anyone with the link”, choose “New and existing guests – guests must sign in or provide a verification code.”
• This keeps external sharing functional but avoids completely anonymous access links.

2. Change default link permissions:

• Under “Choose the permission that is selected when sharing links,” switch from Edit to View.
• Users can still change to Edit when needed, but View is safer as the default.

These two tweaks go a long way toward reducing accidental over‑sharing and data leakage. They’re also concrete examples you can point to when auditors ask how you manage file sharing risks.

What I see over and over is:

• A one‑time hardening project (often after a scare or near‑miss)
• Neatly configured Conditional Access and SharePoint settings
• Then… six months of changes: new admins, new apps, new requirements

Slowly but surely:

• Someone weakens MFA rules for “just one group.”
• A new region is added and not covered by existing location policies.
• A legacy protocol is re‑enabled for a “temporary” workaround.
• SharePoint site owners fiddle with sharing policies.

By the time of the next m365 security assessment or external audit, your environment no longer aligns with your own documented baseline, let alone the CIS benchmark.

That’s why organizations are moving from one‑off projects to continuous microsoft 365 compliance automation.

Manually checking 129 CIS Microsoft 365 Foundations Benchmark controls across Entra ID, Exchange, SharePoint, and related workloads is, frankly, unrealistic on a recurring basis.

This is where automated compliance m365 tooling comes in. A good example in the Microsoft 365 ecosystem is ConfigCobra, which is purpose‑built for this exact problem.

How tools like ConfigCobra help:

• Automated CIS assessment: It continuously checks your Microsoft 365 configuration against all 129 CIS Microsoft 365 Foundations Benchmark controls, with support for Level 1 (essential) and Level 2 (enhanced) profiles.
• Scheduled m365 security audits: You can run assessments daily, weekly, or monthly instead of only before an audit panic.
• Configuration drift detection: When someone changes a Conditional Access policy, enabling a risky setting or weakening MFA, the tool can flag that quickly instead of months later.
• Audit-ready reporting: It generates PDF reports with evidence, pass/fail status per control, and remediation guidance—gold for microsoft 365 audit preparation.
• Multi‑framework mapping: CIS controls can be mapped to NIS2, SOC 2, ISO/IEC 27001, HIPAA, PCI DSS, NIST CSF, etc., so one set of checks supports many regulatory obligations.
• Custom rule sets: If you have internal standards beyond CIS—say specific GDPR, NIS2 or internal policy requirements—you can encode those as custom rules and include them in your automated M365 compliance assessment.

In other words, instead of just “we set CA07 once,” you move to “we continuously verify our Microsoft 365 against CIS and our own policies, and we have the evidence.”

While there isn’t a literal badge called “cis certified microsoft 365” issued by CIS themselves for every tenant, many organizations aim for a posture that is functionally equivalent:

• They adopt the CIS benchmark Microsoft 365 guide as their baseline.
• They document how their Conditional Access, authentication, and sharing settings align.
• They run continuous automated assessments with tools like ConfigCobra.
• They use the reports as part of their ISO 27001, SOC 2, or NIS2 evidence packs.

For auditors and regulators, that combination of standards alignment + automation + evidence is far more compelling than screenshots from last year.

It’s also a much saner way to run Microsoft 365 at scale—especially when you operate in multiple regions and under multiple regulatory regimes.

If you’re wondering where to start tomorrow morning, a practical order might be:

1. Document your target: Decide that CIS Microsoft 365 Foundations is your baseline.
2. Harden identity first: MFA, legacy auth, Conditional Access basics.
3. Lock down locations and devices: Approved countries, compliant devices, supported platforms.
4. Tighten admin and app governance: Admin center access, tenant creation, app consent.
5. Fix sharing defaults: SharePoint/OneDrive sharing and link permissions.
6. Introduce automation: Deploy a tool like ConfigCobra to run ongoing CIS-based assessments and generate reports.

This way, you’re not just doing random security tweaks—you’re building toward a measurable, auditable, and maintainable state.