Active Directory Health Checks Before Migrating to Azure AD Connect

Transitioning to Azure AD Connect is more than just another item on your IT roadmap—it’s the instant when your on-premises identity world connects to the cloud. When the sync goes smoothly, identity feels transparent. Everyone signs in without friction, systems work as expected, and security becomes easier to manage. But if there’s something wrong in your Active Directory (AD)—old objects, DNS irregularities, replication latency, vestigial problems with schema—Azure AD Connect will help spread the poison.

You can consider Azure AD Connect as an interpreter that’s being very rigid. It absorbs what your Active Directory provides and delegates it to Azure AD. If your AD is clean, you’re going stable hybrid identity model. If you have a dirty AD, sync issues, identity errors, auth interruptions and inconsistent UX come in pretty fast.

That is why an extensive Active Directory health check is mandatory before the deployment of Azure AD Connect. The objective is straightforward: check out AAD Connect pre-requisites and test identity sync readiness in order to prevent a cascade of unnecessary issues by starting the migration!

Here’s a structured walk through of what should be included in a full AD health assessment before you roll out Azure AD Connect.

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1. Start with the Foundations: Domain and Forest Health

You can’t build a reliable hybrid identity environment on a shaky AD foundation. Before anything else, confirm that your baseline AD health is sound.

Check Domain and Forest Functional Levels

Azure AD Connect supports a wide range of domain functional levels, but older environments often have underlying limitations. Ensure that:

• The forest level meets at least Windows Server 2003 or higher (which almost all modern deployments exceed).
• Domain controllers (DCs) are not running unsupported or end-of-life Windows Server versions.
• SYSVOL is using DFS-R replication instead of legacy File Replication Service (FRS), as FRS is deprecated and unsupported in hybrid identity scenarios.

Assess Schema Integrity

Azure AD Connect extends the schema with additional attributes. If the schema has inconsistencies or previous extension failures:

• Schema updates may not apply properly.
• Azure AD Connect installation may fail.
• Synchronization can cause attribute-level issues.

Running a schema integrity check now avoids operational surprises later.

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2. Validate Active Directory Replication Health

Replication tends to be one of the biggest silent troublemakers in older or distributed AD environments. Azure AD Connect pulls data from a DC and assumes that the information is consistent across the forest. If replication is broken, stale or conflicting information gets synced to Azure AD.

Key Checks Include:

• No lingering objects between domain controllers.
• Replication latency within acceptable thresholds.
• No failed inbound/outbound replication partners.
• All domain controllers visible and resolvable.

Azure AD Connect cannot “fix” replication issues—if anything, it exposes them quickly. Getting replication under control is mandatory for identity sync readiness.

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3. DNS Integrity and Naming Stability

DNS is the nervous system of Active Directory. Before preparing your environment for Azure AD Connect, verify that DNS is behaving properly.

DNS Checklist:

• DCs register correct DNS records (especially SRV records).
• Clients and servers point to internal DNS—not external providers.
• Reverse lookup zones exist and have correct PTR records.
• No duplicate or stale A records for domain controllers.
• AD-integrated zones are replicating properly.

If DNS is unreliable on-prem, your hybrid identity will inherit the same instability.

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4. Identify and Clean Up Stale Objects

Azure AD Connect syncs all objects unless you explicitly filter them. The average AD environment has years’ worth of:

• Disabled users
• Computer accounts not used for years
• Service accounts with outdated metadata
• Unmanaged groups

Migrating these unnecessary objects creates clutter in Azure AD and increases the risk of synchronization conflicts.

What to Clean Up:

• Remove or archive unused user and computer accounts.
• Align naming conventions where needed.
• Review group nesting structures.
• Validate security vs. distribution groups.

This step directly improves the quality of the cloud identity environment you’re about to build.

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5. Confirm Attribute Health and Consistency

Azure AD Connect relies heavily on specific attributes—especially UPN, sAMAccountName, mail, and proxyAddresses. If these attributes are inconsistent or incorrectly formatted, users will experience login issues immediately after migration.

UPN Health

• UPN should match the domain you plan to use in Azure AD.
• Avoid non-routable UPN suffixes like .local.
• Ensure uniqueness across the forest.

Email and Proxy Address Validation

• Duplicate proxyAddresses attributes cause hard sync failures.
• Primary SMTP addresses must be unique and properly formatted.

sAMAccountName Considerations

• While Azure AD Connect does not rely on sAMAccountName for sign-in, conflicts may still create sync warnings.
• Ensure no illegal characters or unexpected formats.

ObjectGUID and ImmutableID

Azure AD Connect uses ObjectGUID as the anchor attribute. Ensure:

• No manipulated ObjectGUID values.
• No orphaned objects with conflicting anchors.

Clean attributes equal clean synchronization.

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6. Review Organizational Unit (OU) Structure and Sync Scope

Azure AD Connect allows you to pick exactly which OUs to synchronize. This becomes much easier—and much safer—if OUs are well-organized.

Best Practices Include:

• Organize users, devices, and service accounts into clear OU hierarchies.
• Separate stale or archived accounts from active ones.
• Ensure GPO-heavy OUs are not unnecessarily included in the sync scope.

A well-planned OU structure dramatically simplifies the long-term management of your hybrid identity ecosystem.

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7. Assess Group Policy Impact

Group Policies influence authentication, password requirements, Kerberos behavior, login scripts, and device management. Some older GPOs or unsupported settings may conflict with hybrid identity or cloud authentication flows.

Review Policies Related To:

• Password and lockout policies
• Kerberos ticket settings
• Interactive login restrictions
• Credential management rules

This is not about rewriting all your GPOs—it’s about ensuring none of them interfere with cloud-based sign-ins or your future security roadmap.

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8. Confirm Password Hash Sync, Pass-Through Authentication, or Federation Prerequisites

Depending on your authentication choice, different readiness checks apply.

Password Hash Sync (PHS)

• Ensure DCs support required encryption and hashing mechanisms.
• Confirm no outdated password policies conflict with cloud sync.

Pass-Through Authentication (PTA)

• Firewall rules must be validated so agents can communicate securely.
• High availability requires multiple PTA agents.

Federation (AD FS)

• Certificate health must be validated.
• Web Application Proxy endpoints need successful reachability.

Choosing the right authentication model is one part; preparing AD for it is another.

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9. Validate Networking and Firewall Requirements

Azure AD Connect requires secure outbound connectivity to multiple Microsoft endpoints. Before deployment:

• Confirm outbound ports 443 and required URLs are accessible.
• Review any deep packet inspection tools that may disrupt traffic.
• Validate proxy configurations if used.

Misconfigured outbound rules commonly cause sync failures or throttling issues after deployment.

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10. Review Existing Azure AD Environment for Conflicts

Preparing AD is only half the puzzle. Before syncing identities, check Azure AD for:

• Duplicate user objects created manually or through previous sync attempts.
• Conflicting usernames or email addresses.
• Incorrect domain configuration.
• Incomplete or partially verified custom domains.

This ensures that when objects sync, they merge correctly and do not create duplicate identities.

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11. Run Microsoft’s Identity Health Tools

Before Azure AD Connect deployment, Microsoft provides several tools that help assess readiness:

• IdFix: Scans AD for formatting and synchronization errors.
• dcdiag: Evaluates domain controller health.
• repadmin: Checks replication status and identifies failures.
• Azure AD Connect Health (post-install): Monitors ongoing identity health.

Running these tools early gives visibility into issues you can fix before they become production problems.

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12. Document the Findings and Prepare a Remediation Plan

A proper health check doesn’t end with discovery—it ends with a remediation blueprint. The plan typically includes:

• Issues found
• Impact on Azure AD synchronization
• Remediation priority
• Owner for each fix
• Estimated timelines
• Dependencies

This avoids rushed or piecemeal fixes and ensures the migration is controlled and predictable.

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Conclusion

Migrating to Azure AD Connect is about much more than just standing up a sync tool—it’s the start of a hybrid identity journey that will dictate how your users log in to resources for many years. A comprehensive Active Directory health check guarantees identity sync readiness, prevents costly outages, and produces a predictable, healthy Azure AD environment on day 1.

By verifying AAD Connect prerequisites, cleaning up your directory, remediating the actual AD and ensuring a healthy identity infrastructure you significantly improve the reliabilty and security of your hybrid configuration. A clean AD ensures a clean cloud identity experience—and that’s what all of this is really about: smooth operations, minimized risk, and scalable over time.