If you decided to move from one SharePoint account to another, or want to perform a SharePoint tenant to tenant migration, then ensuring a precise transition of permissions, metadata, settings, and data becomes one of the biggest SharePoint migration challenges. Today, I’ll let you know how to overcome these issues with the right planning and tested solutions, which I’ve learned from recent projects.
So, first, let me explain the different types of issues in this migration.
Types of SharePoint Migration Issues
For a clear understanding, I divided challenges into parts:

- Structural issues
Folders, paths, naming, information architecture
Broken inheritance, item-level access, group sprawl
- Metadata issues
Content types, columns, and version history loss
- Customisation issues
InfoPath, Designer workflows, custom pages
- Integration issues
Power Automate, Power Apps, Teams, third-party tools
- Performance issues
Large lists, indexing, throttling, bandwidth
All these issues can be resolved with proper planning and methods, which I’ll share further.
SharePoint Migration Challenges – How to Resolve Them
Here are the common issues faced by users, with their solutions to get rid of them:

#1. Messy Permission Inheritance
Broken inheritance at multiple levels leads to access problems after migration. To resolve this, you have to:
- Audit permissions at site, library, folder, and item levels
- Remove unnecessary unique permissions
- Migrate permissions only after cleanup
- Always ensure your migration solution migrate SharePoint site to another site along with permissions and settings.
#2. Deep Folder Structures and Long Paths
Nested folders exceed limits and cause failures. To overcome this:
- Run path-length analysis
- Flatten folders
- Replace folders with metadata and views
- Shorten names before migration
#3. Unsupported Customizations and Legacy Artifacts
Problem user’s face:
- InfoPath forms
- SharePoint Designer workflows
- Custom master pages
- Blocked file types
Solution:
- Replace InfoPath with Power Apps or Forms
- Rebuild workflows in Power Automate
- Recreate pages using modern web parts
- Isolate blocked files
- Isolate blocked files
#4. Metadata and Version History Loss
Loss of:
- Authorship
- Versions
- Content types
- Columns
This is one of the biggest SharePoint migration challenges, in this case:
- Map content types and columns beforehand
- Test with pilot libraries
- Use tools that preserve metadata and versions
#5. Massive Data Volumes
Slow migration due to throttling and bandwidth limits. Here’s how to resolve:
- Migrate in batches
- Schedule off-hours jobs
- Use incremental migration
- Monitor retry and throttle logs
#6. Integrations Breaking After Transition
Due to integration failure, user’s expierenced this type of issues:
- Power Automate flows fail
- Power Apps lose connections
- Teams tabs break
To bypass these, follow these stepwise instructions:
- Document integrations before migration
- Reconnect to new URLs
- Reconfigure Teams tabs
- Test each integration
#7. Poor Information Architecture
Migrating old chaos recreates the same chaos. So:
- Redesign the architecture before migration
- Use hub sites
- Organise by function
- Transfer into a cleaner structure
#8. Site URLs, Domains, and Broken Bookmarks
Many times, old links and bookmarks stop working. To resolve this:
- Plan URL structure in advance
- Communicate changes
- Use redirects where possible
- Update important embedded links
#9. Large Lists and Libraries Hitting Threshold Limits
Libraries with over 5,000 items cause performance issues. That’s why:
- Index columns
- Split large libraries
- Use filtered metadata views
#10. Orphaned and Redundant Data (ROT Data)
Unnecessary data increases time and risk. So:
- Run cleanup campaigns
- Archive SharePoint site that is not in use
- Migrate only relevant data
#11. Inconsistent Naming Conventions
Random names create confusion post-migration. This creates a huge problem when it comes to management:
- Define naming standards
- Rename key sites and libraries
- Apply consistency going forward
#12. Performance Issues After Migration
Slow libraries and search complaints are common after the transition. Here’s how to fix them:
- Reindex sites and libraries
- Optimize views
- Remove unnecessary columns
#13. Choosing the Wrong Migration Approach
Basic tools used for complex environments cause data and permission loss. After dealing with the challenges above, I’ve learned that manual methods and basic tools are not enough to move documents from one SharePoint site to another, with files and other data. To bypass all the hassles related to this transition, I opt for a professional solution like the SharePoint Online Migration Tool to ensure zero risk of data loss and preserve data integrity.
Why do I recommend this?
- Migrates site, library, folder, and subsites
- Preserves permission inheritance and unique permissions
- Supports proper user and group mapping between environments
- Migrates columns, content types, and document properties
- Uses incremental and delta migration
- Allows batch-wise migration by sites or libraries
- Allows real-time tracking success, failures, and skipped items
Why does this matter?
Most migrations fail because:
- Metadata wasn’t preserved
- Permissions broke
- Integrations failed
- The folder structure caused errors
- No visibility into what was actually migrated
Using a professional tool bypasses all these issues.
Now, Follow the Step-by-Step Instructions for the Hassle-Free Transition
- Step 1. Install the above-mentioned solution and mark Microsoft 365 as both the source & target platform.

- Step 2. Check the Sites, Document Library, and Lists boxes.

- Step 3. Now, provide the Admin email ID & Application ID for both source and destination tenant or account.

- Step 4. Afterwards, click on the Fetch Users, Import Users, or Download Template to map the source users. Do the same for SharePoint sites.

- Step 5. Hit the Start Migration button to initiate the procedure.

So, try this solution now, and get the expected results from the transition. To ensure a hassle-free migration, always follow the SharePoint Online migration checklist.
Author’s Verdict
SharePoint migration challenges are structural and human at the same time. I make migrations smooth by:
- Cleaning permissions before moving
- Replacing folders with metadata
- Testing before full migration
- Opting for a reliable migration utility
This makes a SharePoint transition a breeze!
Overall, to bypass any SharePoint migration issues, remember only two points:
- Proper planning
- Appropriate transition tool
Validating this checklist ensures a hassle-free migration within the expected time.
People Also Ask
Q. Can I migrate SharePoint permissions exactly?
Yes, with the mentioned solution, it is possible to move permissions simultaneously. But if you’re using a manual solution, then it is impossible to do so, as there is no legacy method to transfer permissions from one account to another.
Q. Do SharePoint alerts and notifications move during migration?
No. Alerts set by users on libraries, lists, or items do not migrate. Users must recreate them after migration.
Q. What happens to checked-out documents during migration?
Checked-out files fail to migrate. Make sure all documents are checked in. Before starting, always validate check in and check out in SharePoint before transition.
Q. Does the recycle bin content get migrated?
No. Items in first-stage or second-stage recycle bins are not migrated. So, restore anything important before migration.