^{Original article published on April 22, 2024}

Microsoft Intune can be a game-changer for IT teams when it’s configured correctly. But without a strategic rollout, it’s easy to fall into traps that create more work, not less. Below, we walk through where teams typically go wrong and how to steer clear.

Where Intune Deployment Can Go Wrong

Rolling out Intune without a roadmap is like deploying firewalls without rules, you’re technically “secure,” but effectively blind.

Costly mistakes, hidden risks
Intune isn’t a plug-and-play security blanket. Missteps—like skipped Conditional Access or forgotten compliance policies—can leave sensitive data exposed to bad actors or land your org in hot water with auditors. In many cases, these aren’t visible until it's too late.

Failing to plan also creates operational chaos:

• Devices go unmanaged
  
• App updates stall
  
• Employees get locked out or misconfigured
  
• Security teams waste time chasing down false positives or missed alerts
  

This isn’t just a tech hiccup—it’s a business liability.

The financial risk is real
From HIPAA to PCI-DSS, fines for non-compliance are steep. Even a single misconfiguration—like not enforcing device encryption—can mean thousands in penalties or lost contracts. Add to that the internal cost of remediation, user downtime, and reputational damage? You’re easily looking at six figures.

The fix: proactive planning
The earlier you get your arms around Intune configuration, the more control you gain. That means policy versioning, test groups, scheduled audits, and integrations that support your workflows—not generic defaults.

Common Mistakes to Avoid with Intune Deployment

These aren’t rare slip-ups. They’re patterns. And they’re all fixable, with the right awareness and planning.

1. Skipping conditional access setup
Without Conditional Access, any device, even a jailbroken iPhone or an unmanaged laptop, could connect to sensitive apps if the user credentials are valid. That’s a dangerous gap, especially when phishing is rampant.

Caveat: Many orgs skip this step to avoid support headaches. But Microsoft lets you run Conditional Access in “report-only” mode first, so you can validate rules before enforcement. There’s no excuse to fly blind.

2. One-and-done policy configuration
Too often, teams treat Intune like a set-it-and-forget-it tool. Policies get created during deployment and never revisited—even as the org adopts new apps, hires new teams, or rolls out new hardware.

Caveat: Static policies quickly become mismatched to real-world usage. Worse, outdated configurations can actually block compliance or trigger user friction. Set a calendar reminder: quarterly policy audits should be as routine as patching.

3. Firewall misconfigurations
A surprisingly common issue: Intune appears “broken” because critical traffic is blocked. Firmware updates or routine changes to firewall rules often close the ports Intune needs to deliver policies, app deployments, or telemetry data.

Caveat: Firewall settings aren’t always in IT’s hands—especially in large orgs or hybrid environments. Publish and circulate a firewall checklist aligned to Microsoft’s latest endpoint and IP recommendations.

4. Weak or misconfigured MFA
Multifactor authentication (MFA) is your frontline defense—but not all MFA is created equal. A common mistake is enabling SMS-based MFA for admin accounts (which can be phished) or forgetting to enforce it on legacy portals.

Caveat: MFA should include strong methods like push notifications or FIDO2 keys. And don’t forget emergency/break-glass accounts—leave them exposed, and you’ve got a hidden backdoor.

5. Granting too many admin rights
It starts innocently—granting a few folks full access “just to get things working.” Suddenly, everyone’s in the Global Admin group, and security review flags your Intune setup as a privilege escalation disaster.

Caveat: Even Microsoft recommends using Privileged Identity Management (PIM) to grant temporary admin rights on-demand. Always follow the principle of least privilege—no one should be admin “just in case.”

6. Compliance policies misconfigured
This one’s subtle: you think your devices are compliant… but they’re not. Why? Because the compliance policy requires BitLocker, or a specific OS version, and no one tested that the profile applied successfully.

Caveat: Don’t just assume policies work. Check enforcement logs and compliance dashboards. Better yet, set up test user/device groups to verify policies before pushing globally. And always communicate what compliance means to end users—it’s not obvious to them.

Why Best Practices Are Your Best Bet

Best practices for Microsoft Intune deployment aren’t just IT formalities—they translate into measurable wins across the business.

Faster productivity means your users get the right apps, access, and updates without delay. BYOD (Bring Your Own Device) flexibility empowers employees without sacrificing security. And when you cut down on agent bloat and helpdesk tickets, your team finally gets to work on the important stuff. Done right, Intune becomes less of a daily burden and more of a force multiplier.

Intune Best Practices from the Start

The problems above aren’t fatal—but they do require focused remediation. Here’s how to fix them right.

1. Define conditional access from Day 1
Set clear guardrails that adapt to user location, device compliance, and risk signals. Start with simple conditions like “only allow access from Intune-compliant devices” and build from there.

Caveat: Too many access rules too early can lock out legitimate users. Roll out in “report-only” mode first to test impact, then enforce.

2. Schedule policy reviews like patch cycles
Just like software updates, Intune policy configurations should be reviewed regularly. Use quarterly checkpoints to audit MAM (Mobile Application Management) and MDM (Mobile Device Management) settings against new threats or business changes.

Caveat: Avoid “policy sprawl.” Document what each policy is for, and prune deprecated ones before they pile up.

3. Maintain an approved firewall rule set for Intune
Keep a living list of required ports, IPs, and services for Intune operations. Align firewall teams and security teams to prevent well-meaning changes (like firmware upgrades) from breaking device sync or telemetry.

Caveat: Cloud services like Intune occasionally update IP ranges. Subscribe to Microsoft’s service tag updates to avoid playing catch-up.

4. Enforce MFA with strong fallback options
Use Microsoft Entra ID (formerly Azure AD) to enforce MFA on all administrator accounts. Leverage phishing-resistant options like FIDO2 or Microsoft Authenticator with push approval.

Caveat: Don’t forget your break-glass accounts—ensure these are monitored and MFA-enabled with extra controls.

5. Use role-based access—not blanket admin rights
Use Entra ID groups and Intune RBAC (role-based access control) to assign permissions by job function. Lock down global admin access and require just-in-time (JIT) elevation via Privileged Identity Management (PIM).

Caveat: RBAC takes planning. Map out responsibilities early to avoid a “flat” model where everyone gets too much access.

6. Build compliance policies with built-in remediation
Leverage Intune’s compliance engine to check OS versions, encryption status, and app presence. More importantly, configure remediation actions—like isolating non-compliant devices or alerting IT.

Caveat: Be careful with harsh remediation like blocking access outright. Start with warnings, escalate only after validation.

Get a Little Help with Intune Deployment Best Practices

You may have bigger things to do than babysit Intune deployment. That’s why Hypershift takes the complexity off your plate—from architecture to ongoing support.

Whether you’re integrating with SCCM, migrating from another MDM, or just trying to get your compliance house in order, we’ve done it. With over 160 financial institutions and enterprise clients on our roster, we know the path and the potholes.

Check out our Managed Services to see more of what we can offer.

Contact our Microsoft services team to assess your current setup or map out a smarter deployment plan.