Business changes like mergers, acquisitions, divestments, or brand transitions often require moving users from one Microsoft 365 tenant to another. While Microsoft does provide a native way to migrate mailboxes between tenants, the process is anything but simple. It demands extensive planning, advanced PowerShell usage, strict licensing control, and careful coordination between administrators.
This guide explains:
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What a manual cross-tenant mailbox migration involves
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Required licenses, permissions, and setup
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Step-by-step overview of the native migration workflow
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Key challenges administrators commonly face
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How MailsDaddy simplifies tenant-to-tenant migration
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Best practices and final recommendations
1. Understanding Manual Cross-Tenant Mailbox Migration
Manual tenant-to-tenant mailbox migration uses Microsoft’s built-in Exchange Online capabilities to move mailbox data from a source tenant to a target tenant. The data typically includes:
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Emails
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Calendar entries
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Contacts
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Tasks and notes
The migration relies heavily on:
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Exchange Online PowerShell cmdlets
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Organization relationships between tenants
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Migration endpoints
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CSV-based mailbox mapping for bulk moves
It’s important to note that this method focuses only on mailbox data. Services such as Microsoft Teams chats, OneDrive files, SharePoint sites, and some archive mailboxes are not migrated unless handled separately with additional tools or processes.
2. Licensing and Prerequisites
2.1 Cross-Tenant Migration Licensing
Each user involved in a cross-tenant mailbox migration requires a Microsoft cross-tenant migration license. This is a one-time add-on license available with most Microsoft 365 plans, including Business, E3/E5, and frontline subscriptions.
2.2 Administrative Roles
Admins need elevated permissions to perform the migration. Typically, Global Administrator and Exchange Administrator roles are required. Since this is a cross-tenant operation, coordination between administrators of both tenants is mandatory.
2.3 Azure AD Application Setup
In the target tenant, an Azure AD application must be registered to authorize mailbox migrations:
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Configure the app for multi-tenant access
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Set the redirect URI to
https://office.com -
Assign the Mailbox.Migration application permission
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Grant admin consent
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Generate and store a client secret
The application ID and secret are later used in PowerShell commands.
2.4 Organization Relationship and Migration Endpoint
An organization relationship must be created to allow inbound mailbox moves. Additionally, an Exchange Online migration endpoint is configured, referencing the Azure AD app credentials.
3. Overview of the Manual Migration Process
Below is a high-level view of how administrators typically perform a native tenant-to-tenant mailbox migration.
3.1 Source Tenant Preparation
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Create a mail-enabled security group to control migration scope
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Export mailbox attributes such as Exchange GUID, Archive GUID, LegacyExchangeDN, and email addresses
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These values are used to correctly match mailboxes in the target tenant
3.2 Target Tenant Preparation
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Create MailUsers for each source mailbox
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Assign temporary passwords and match Exchange GUIDs
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Apply the cross-tenant migration license to each MailUser
3.3 Configure Trust and Endpoint
Using Exchange Online PowerShell:
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Establish an organization relationship allowing inbound mailbox moves
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Create a migration endpoint using the Azure AD app credentials
3.4 Run Migration Batches
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Prepare a CSV file mapping source mailboxes to target mailboxes
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Create and start migration batches via PowerShell
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Monitor progress using migration statistics cmdlets
Once completed, source mailboxes are converted into MailUsers to maintain mail routing.
3.5 Post-Migration Tasks
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Update DNS records and allow changes to propagate
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Disable inbound mail flow in the source tenant
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Assign full Microsoft 365 licenses to target users
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Validate Outlook connectivity, Autodiscover, and mail flow
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Inform users that Outlook profiles may need to be recreated
4. Challenges of the Native Migration Method
While the native approach avoids third-party costs, it introduces significant complexity. Administrators often face:
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Extensive PowerShell scripting and troubleshooting
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CSV errors and mismatched GUIDs
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Time-consuming validation and rollback efforts
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Limited scope restricted mainly to Exchange Online mailboxes
For larger environments, these challenges quickly translate into higher risk, longer timelines, and increased support overhead.
5. Why MailsDaddy Cross-Tenant Migration Stands Out
MailsDaddy Tenant to Tenant Migration Service is designed to eliminate the complexity of manual migrations while offering far broader coverage.
Comprehensive Data Migration
MailsDaddy supports migration of:
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User and shared mailboxes
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Archive mailboxes
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OneDrive and SharePoint data
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Microsoft Teams files and channels
Streamlined Workflow
The process is simplified into clear stages:
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Automatic discovery and environment assessment
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User mapping via UI or spreadsheet
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Secure OAuth 2.0 authentication
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Pre-stage migration followed by incremental delta sync
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Controlled final cutover with retry and throttling logic
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Real-time dashboards and progress reports
Security and Accuracy
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Preserves mailbox metadata, timestamps, and permissions
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Uses 256-bit encrypted data transfer
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Provides detailed audit logs and migration reports
Minimal Business Disruption
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Near-zero downtime for end users
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Assistance with Outlook profile reconfiguration
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Dedicated post-migration validation and support
Higher ROI
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Migration timelines reduced from weeks to days
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Eliminates manual scripting and error handling
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Ideal for complex, multi-domain, or hybrid environments
Unlike the native method, which focuses narrowly on mailboxes, MailsDaddy delivers a true end-to-end tenant migration experience.
6. Best Practices for a Successful Migration
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Perform detailed user and data mapping early
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Run a pilot migration before full rollout
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Ensure licenses are assigned in advance
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Lower MX record TTL before cutover
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Maintain backups of critical data
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Communicate changes clearly to end users
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Schedule cutover after final delta sync
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Verify mail flow and Outlook connectivity post-migration
7. Final Verdict
Native Microsoft Approach
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Suitable for small, simple migrations
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Requires advanced PowerShell knowledge
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Limited scope and higher risk of errors
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Significant administrative effort
MailsDaddy Cross-Tenant Migration Service
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Migrates mail, archives, OneDrive, SharePoint, and Teams
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Secure OAuth-based authentication
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Automated, metadata-preserving, and scalable
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Saves hundreds of admin hours and reduces risk
In simple terms:
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Native migration is like assembling furniture manually—possible, but time-consuming and error-prone
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MailsDaddy is the fully assembled solution—efficient, reliable, and stress-free
If you’re looking for a secure, automated, and enterprise-ready Microsoft 365 tenant-to-tenant migration without scripting headaches, MailsDaddy Cross Tenant Migration Service is the smarter choice.
Also Read: Manual Microsaoft 365 Ternant to Tenant Migration
