Active Directory Migration to Entra: 5-Phase Complete Checklist

Active Directory migration to Entra is one of the most consequential infrastructure decisions a mid-market IT team will make this decade, and most organizations underestimate what it actually takes. This article walks through five realistic phases, names the specific things that slow teams down, and points to the tooling that actually helps.

What Active Directory Migration to Entra Really Involves

Moving to an Entra-only identity model means more than pointing your devices at a new directory. It means eliminating your reliance on on-premises Active Directory for authentication, device management, group policy, and application access. Some organizations get there cleanly. Most discover mid-project that they have a 15-year-old line-of-business app that speaks only Kerberos, three file shares nobody documented, and a VP who considers domain-joined laptops a personal safety blanket.

Honest planning prevents those surprises from becoming project killers. Here is what the work actually looks like.

Phase 1: Inventory and Dependency Mapping

You cannot migrate what you have not catalogued. Start with a full export of your AD environment: user accounts, computer objects, groups, organizational units, service accounts, and GPO linkages. Microsoft's Microsoft Entra Connect documentation covers the sync architecture in detail, and the built-in AD Assessment in Azure Arc gives you a scored readiness view.

Beyond the directory itself, map authentication dependencies across every application. You are looking for three specific signals:

• NTLM or Kerberos authentication calls in web or desktop apps
• UNC path dependencies to on-premises file shares
• Group Policy Objects that configure security baselines, drive maps, or software deployment

This phase takes longer than people expect. A 500-seat organization with a decade of organic AD growth can easily have 300+ GPOs and 40+ service accounts, many of them undocumented. Block two to four weeks here before touching anything else.

Phase 2: Device Management Transition

Most hybrid environments have devices in one of three states: domain-joined only, Hybrid Azure AD Joined (HAADJ), or Azure AD Joined (now called Microsoft Entra Joined). The goal is to move everything to Entra-joined and managed entirely through Microsoft Intune.

HAADJ is a transitional state, not a destination. Devices in that state still have a hard dependency on line-of-sight to a domain controller for certain operations. Moving them to Entra-joined requires:

• Validating that all required apps work without domain trust
• Confirming that local administrator workflows are handled through Entra Local Administrator Password Solution (LAPS) or a Privileged Access Workstation model
• Migrating software deployment to Intune or a third-party MDM that supports Entra-joined devices

For organizations with a large installed base of Windows 10 or 11 devices, the Autopilot reset path is the cleanest option for reprovisioning without re-imaging. Plan for a phased rollout by device type, starting with new employee builds, then moving to refresh cycles.

Phase 3: Application Authentication Modernization

This is where most Active Directory migration to Entra projects hit their first serious wall. Applications that rely on Kerberos or NTLM cannot authenticate against Entra ID natively. You have four real options:

• Rewrite or upgrade the app to support modern authentication (OAuth 2.0 / OpenID Connect). Best outcome, highest cost.
• Use Microsoft Entra Application Proxy to publish the app externally while the backend still uses Kerberos via Kerberos Constrained Delegation. This buys time without a full rewrite.
• Migrate to a SaaS equivalent that already supports Entra. Often the right call for legacy ERP or CRM tools approaching end-of-life.
• Keep a minimal AD footprint specifically for apps that cannot be modernized, and treat that domain as a managed exception with a clear sunset date.

Third-party identity governance platforms, including Saviynt, SailPoint, and Omada, can help you map application entitlements and flag high-risk accounts during this phase. They are not required, but they reduce manual spreadsheet work considerably on environments above 1,000 identities.

Phase 4: Group Policy Migration to Intune

Group Policy is the deepest cultural attachment most IT teams have to Active Directory. It works, people understand it, and it has been the answer to every Windows configuration question since Windows 2000. But GPO cannot follow Entra-joined devices.

Microsoft's Group Policy Analytics tool in Intune is the right starting point. Import your GPOs and it will tell you which settings map directly to Intune configuration profiles, which require Settings Catalog equivalents, and which have no current Intune equivalent.

In practice, roughly 60 to 70 percent of common GPO settings have a direct Intune equivalent. The remaining 30 percent need remediation scripts, custom OMA-URI settings, or a policy decision that the setting is no longer needed. Do not try to port every GPO one-for-one. Treat the migration as a configuration review. Some of those policies were created in 2011 and nobody remembers why.

The open-source community has contributed useful tooling here as well. The PolicyAnalyzer tool from the Microsoft Security Compliance Toolkit is free, and community-maintained PowerShell modules on GitHub can help bulk-export GPO settings into a format that accelerates the comparison process.

Phase 5: Decommission Planning

The final phase is the one teams put off the longest, because it is the one that feels permanent. Decommissioning your last domain controller is the proof point that the migration succeeded. It is also the phase most likely to be delayed by political resistance rather than technical blockers.

Structure decommission in stages:

• Demote secondary domain controllers first, monitoring for any authentication failures over a 30-day window
• Redirect any remaining DNS-dependent services away from AD-integrated DNS zones
• Confirm that SYSVOL replication and netlogon dependencies are fully removed from all endpoints
• Archive AD backups per your data retention policy before taking the final domain controller offline

The NIST SP 800-207 Zero Trust Architecture guidance is a useful reference for framing the decommission conversation with leadership. Moving to Entra-only is not just a technology decision. It is a meaningful step toward a verifiable zero trust posture, and framing it that way often helps move political blockers.

What Actually Slows Teams Down

Three things account for most delays in an Active Directory migration to Entra project, and none of them are primarily technical.

Legacy line-of-business applications with no upgrade path and no vendor support are the most common culprit. The honest answer is that some of these apps will outlive your migration timeline, and you need a documented exception process for them rather than letting them block everything else.

On-premises file shares that have grown organically for years are the second. Migrating file share access to SharePoint Online or Azure Files requires permission remediation work that most teams underscope by a factor of three.

Political resistance is the third and least discussed. Domain-joined infrastructure represents a control model that some IT professionals have built their entire career around. Change management, executive sponsorship, and clear communication about what Entra does and does not change about day-to-day operations matters as much as the technical roadmap.

A Note on the Tooling Landscape

Microsoft's native tooling covers the core workflow: Entra Connect for hybrid sync, Group Policy Analytics in Intune, AD Assessment via Azure Arc, and the Entra ID Governance features for access reviews and entitlement management. For most organizations under 2,000 seats, that stack is sufficient.

Larger environments or those with complex identity governance requirements often benefit from third-party platforms. SailPoint IdentityNow and Saviynt both offer AD-to-Entra migration acceleration modules. Omada Identity Suite has strong support for role mining, which helps rationalize group structures before migration.

On the open-source side, the IAM community has contributed tools worth knowing. DSInternals is a well-maintained PowerShell module that lets you read AD database internals for audit and migration purposes. ADExplorer from Sysinternals (now part of Microsoft) remains useful for offline AD snapshots. And the broader community around the IETF's SCIM 2.0 standard has produced connectors that help bridge legacy HR systems to Entra during the provisioning modernization phase.

No single tool does everything. The best migrations pair Microsoft's native assessment tooling with whatever fills the specific gaps in your environment, evaluated on merit rather than vendor preference.