How to Merge Folders in SharePoint: Step-by-Step Guide

  Tej Pratap Shukla
Written By Tej Pratap Shukla
Anuraag Singh
Approved By Anuraag Singh  
Modified On January 7th, 2026
Reading Time 9 Minutes Reading

Over time, managing folders in SharePoint can become a difficult task as the teams collaborate and document libraries grow. Because of duplicate folders and scattered files finding the right information on time is difficult. That’s the reason learning how to merge folders in SharePoint is necessary for organising folders in the correct way and enhancing productivity. 

In this article, I am going to explain ways to SharePoint merge folders safely without losing files and permissions. I also share tips to handle large libraries and best practices to avoid common mistakes, aligned with SharePoint document management best practices.

Why Users Need to Merge Folders in SharePoint

I have seen it becomes necessary to merge folders in SharePoint due to poor planning and team collaboration. When multiple departments share the same SharePoint and upload files then it is a common thing that duplicate folders with the same name appear. Here are more reasons:

  • Duplicate project folders created by different users
  • Departmental restructuring
  • Migration from file servers to SharePoint 
  • Cleanup after long-term usage
  • Improving search and navigation

In these scenarios it becomes important to understand how to merge folders in SharePoint to restore order and improve productivity. In a clean folder you don’t get confused and it also speeds up searches, when you find duplicate files in SharePoint Online before starting the process.

Important Things to Know Before SharePoint Merge Folders

Before starting any SharePoint merger, I always check some points to avoid any kind of hassle later. SharePoint behaves differently with Windows Explorer and ignoring these minor things can be the reason for permission and access issues later. Here are key points to keep in mind:

  • Folder-level permissions might get changed after the merger
  • Columns must match between folders
  • Version history should be intact
  • Large folders can be time-consuming

Keeping these factors in mind makes a difference in how to merge folders in SharePoint, when you need to copy files with metadata tags in SharePoint Site. Now that you have understood why there is a need to merge folders in SharePoint and points to know before starting the process, now let’s dive into the method to do it.

Method 1. SharePoint Merge Folders Using Drag and Drop (Basic Method)

Most of the users prefer this method as it works better with small folders. Here are the steps that I follow:

  1. Open the SharePoint document library
  2. Go to the source folder
  3. Select all files inside the folders 
  4. Drag them to the destination folder
  5. Once it done delete the empty folder

Because of its user-friendly steps, and popular among users, but it has limitations in that it is not as effective with large folders with unique permissions. Still good for the quick cleanups and a practical way to understand how to merge folders in SharePoint without any advanced tools. Similarly, you can also understand how to move folders in SharePoint.

Method 2. Use the “Move To” Option

The “Move To” method is better and quicker compared to drag-and-drop. To do so, below are the instructions:

  • Choose all files inside the folder
  • Select the Move to option from the toolbar
  • Go to the destination folder
  • Confirm the move

That’s all! Now, go to the target folder and see if your content is properly moved or not. Opt for this if hierarchy and structure are your first preferences. 

Method 3. How to Merge Folders in SharePoint Using File Explorer Sync

Syncing SharePoint with OneDrive is the best option for many users who are using OneDrive regularly on their systems. For the same, here is the complete set of guidelines:

  • Configure the SharePoint library using OneDrive
  • Open the synced folder on your computer
  • Move files between folders locally
  • Allow OneDrive to sync changes back

Use this solution if you are handling large folders while SharePoint merge folders. So, till now we discussed all the manual methods, which are suitable for all scenarios. Next, I’ll explain more about why they are not go-to.

Handling Permission While Merging Folders

The most common issue that users face including me is broken permissions after merging folders. SharePoint gets permissions from the parent folder, which can pass custom access settings. Here are the best practices that I personally follow to avoid this issue:

  • Thoroughly check permissions before moving files
  • Apply unique permissions again after merging
  • Test access with a user account

Managing permissions in the correct and right way is a key factor in learning how to merge folders in SharePoint especially understanding how to manage SharePoint access from a business perspective.

Merging Folders Across Different Document Libraries

I have seen that in many organisations they require mergers across different libraries or even different sites and this is a hard process that requires proper planning. In such scenarios:

  • Metadata columns need to be the same
  • It is important that content types match accurately
  • Verify that all required permissions are intact

By using these manual methods many organisations struggle. This is where I recommend that they go for professional and trustworthy tools that ease the SharePoint merge process for them.

Professional Approach for Large SharePoint Folder Consolidation

Manual methods are risky and complex when it comes to larger site restructure or migration projects. That’s why I recommend a professional and reliable solution for the same, i.e., SysTools SharePoint Online Migration Tool.

Download Now Purchase Now

It helps you to migrate the folders, files, documents, and even permissions to another tenant or account. 

Not only this, you can move an entire SharePoint site while maintaining metadata. This solution minimizes errors and quickly completes the process of SharePoint merge folders as part of site-to-site migration.

For admins and IT professionals, it is highly recommended to opt for this solution to simplify the process of how to merge folders in SharePoint.

After taking the full version, follow the steps below to merge all folders from the SharePoint site:

Step 1.  Install and open the utility and select Microsoft 365 as both source and target platform.

Install Tool

Step 2.  Scroll down and select Site options

Site option

Step 3.  Now provide your admin credentials, i.e. Admin Email and Application ID. Do the same for destination.

Admin credentials

Step 4.  Afterwards, map the source users via Fetch Users, Import Users, or Download Template.

Source users

Step 5.  Lastly, hit the Start Button to initiate the consolidation process

Start migration

Author’s Verdict

It helps you to migrate the folders, files, documents, and even permissions to another tenant or account. 

Not only this, you can move an entire SharePoint site while maintaining metadata. This solution minimizes errors and quickly completes the process of SharePoint merge folders as part of site-to-site migration.

For admins and IT professionals, it is highly recommended to opt for this solution to simplify the process of how to merge folders in SharePoint.

Common Issues Faced After Merging Folders

Here are some common issues that I came across while merging folders:

  • Files get missing after the merger
    Solution: Instead of moving the files in one go move them in smaller batches and use the Move To method over drag-and-drop.
  • Permissions issues
    Solution: Before merging check if there are unique permissions applied; if they are then reapply them after the merger to prevent access issues.
  • Drop in performance with large folders
    Solution: Avoid the merger in peak hours and split the large files into smaller groups to avoid time out. This makes the process of how to merge folders in SharePoint easier to learn and implement.
  • Duplicate content
    Solution: Go through the folders and remove or rename the duplicates before SharePoint merge folders.

These issues can be avoided by proper planning before the merger and following the solution that is given ensures the process of Sharepoint merger folder is secure and hassle-free. The solution is quick that’s why I recommend a professional solution so that you don’t need to go through all of this, because the process needs to be stress-free.

Best Practices to Merge Folders Safely

Here are the best practices that I follow:

In order to get the smooth process of how to merge folders in SharePoint, follow these points to avoid interrupting the workflow.

Author’s Verdict

In order to maintain a clean and efficient document management system, learning how to merge folders in SharePoint is no longer a choice anymore, it become a necessity. It is important to go with the right approach as per your requirements, it can be either manual drag and drop or a professional solution and following the points before any merger can avoid issues later.

Personally, the manual method is good and free but they have their limitation, which can be a threat to the data. They are good if you want a quick clean-up or want to move small files. In order to move large files it is a good decision go with the professional solution that we have discussed above. When done correctly, SharePoint merge folders improve collaboration and searches are better.

FAQs

Q. How to put a folder in another folder on SharePoint?

You can do that easily by following the “Move To” method.

Q. Why is SharePoint creating duplicate folders after the merger?

It is because the folders are not renamed or removed before the merger.

Q. Is it possible to merge folders in SharePoint Online?

Yes, it is possible as SharePoint Online allows folder merging by moving files between folders

Q. Among all the manual methods which one is reliable and good?

I personally recommned “Move To” method as it is the easiest and most reliable method among all of them.

Q. Does SharePoint merge folders keep permissions?

Yes, but permissions may change due to inheritance so they should be verified after merging.