Best Ways to Recover Deleted Files from Virtual Machine Disks

Virtual machines (VMs) make IT flexible and scalable—but data stored inside is not immune to accidental deletion. Whether you’re running VMware, Hyper-V, or another virtualization platform, losing files can be just as disruptive as on a physical server.

Deleted files from VM disks can derail business operations, delay testing environments, and cause personal projects to grind to a halt.

The good news? In many cases, those files can be recovered. This guide explores proven methods and tools for safely recovering deleted files from virtual machine disks such as VMDK, VHD, and VHDX.

Virtual Machine Disks Explained

What VM Disks Are

• VMware: Uses VMDK files to store VM data.
  
  
• Hyper-V: Uses VHD and VHDX formats.
  
  
• Other formats: QCOW2 (KVM/QEMU), RAW images, and more.
  
  

How Data Storage Works in VMs

Virtual disks function like physical hard drives: they contain partitions, file systems, and data. When files are deleted inside a VM, they aren’t immediately erased. Instead, the file system simply marks that space as available for reuse, which means recovery is often possible—if you act quickly.

Common Scenarios of File Deletion in VMs

File loss in virtual machines can happen in several ways. The most common is accidental deletion inside the guest OS—whether it’s using Shift+Delete in Windows or the rm command in Linux. Another frequent issue arises when a virtual disk partition is mistakenly reformatted, wiping out everything stored on it.

Beyond user errors, technical problems can also cause trouble. A corrupted or orphaned VMDK or VHD file may suddenly make all VM data inaccessible. Similarly, rolling back to an earlier snapshot or checkpoint can overwrite recent work. And in more severe cases, the virtual disk file itself may be deleted from the host system, leaving the entire VM and its contents at risk.

Precautions Before Attempting Recovery

Before starting any recovery process, it’s critical to minimize the risk of further data loss. The first step is to stop writing to the affected virtual disk immediately—every new file or system operation increases the chance of overwriting the deleted data. Instead of working on the original disk, create a cloned copy using tools like dd, Clonezilla, or the export features built into your hypervisor.

It’s also worth checking available snapshots or backups before attempting deeper recovery, as these are often the fastest way to restore lost files. And when inspecting a damaged or corrupted virtual disk, always mount it in read-only mode to avoid making irreversible changes.

Built-in Recovery Options

1. Within the Guest OS

• Recycle Bin or Trash: The easiest place to check first.
  
  
• OS Recovery Tools: Windows File History, macOS Time Machine, or Linux utilities like extundelete.
  
  

2. Hypervisor Features

• VMware Snapshots: Revert to a state before deletion.
  
  
• Hyper-V Checkpoints: Roll back to a previous snapshot.
  
  
• Limitations: These features may overwrite newer data if not carefully used.

File Recovery from Virtual Disks

1. Mount the Virtual Disk on Host

• VMware Workstation/ESXi: Attach the VMDK as a secondary disk.
  
  
• Hyper-V: Mount the VHD/VHDX through Disk Management.
  
  
• Advantage: Lets you treat the VM disk like a standard drive for scanning.
  
  

2. Use File Recovery Tools Inside the Mounted Disk

Once mounted, you can scan the virtual disk with recovery tools, just as you would a physical disk. This is often the most practical method when looking for how to recover deleted files from virtual machine environments, since the tools treat the virtual disk like a standard hard drive.

Examples include:

• Recuva (simple, Windows-focused).
  
  
• R-Studio (supports many file systems, advanced options).
  
  
• DiskInternals VMFS Recovery (for VMware VMFS volumes).
  
  
• Stellar Data Recovery for Virtual Machines.
  
  
• UFS Explorer.
  
  

Key features to look for:

• Support for VM disk formats.
  
  
• Ability to scan by file signatures.
  
  
• Read-only or non-destructive recovery methods.

Specialized Virtual Disk Recovery Tools

Some cases require advanced tools designed specifically for VM environments:

• DiskInternals VMFS Recovery – ideal for VMware ESXi datastores.
  
  
• Stellar Data Recovery for Virtual Machines – supports VMDK, VHD, VHDX, QCOW2.
  
  
• R-Studio – powerful tool for raw recovery across multiple file systems.
  
  
• UFS Explorer Professional Recovery – specialized in handling VM disk structures.
  
  

When to use these tools:

• If mounting fails.
  
  
• If the virtual disk itself is corrupted or deleted.

Advanced Scenarios

In more complex cases, recovery goes beyond simple file restoration. If the virtual disk file itself (such as VMDK or VHD) has been deleted from the host, the first step is to use host-level recovery software to restore that disk image before attempting file-level recovery inside it. Similarly, with split or flat VMDK files, the disk segments need to be reassembled correctly before any meaningful recovery can take place.

Things get even more complicated when the VM is stored on a RAID array or NAS device. In these scenarios, the storage system must be rebuilt first; trying to recover VM files on top of a broken RAID risks permanent data loss. Only after the RAID or NAS is stabilized should you proceed with virtual disk recovery.

Best Practices to Avoid Future Data Loss

• Regular Backups: Maintain both VM-level and file-level backups.
  
  
• Snapshot Management: Don’t rely solely on snapshots as backups.
  
  
• Version Control: Use Git or other versioning tools for critical project files.
  
  
• Test Recovery Plans: Simulate data loss and practice recovery to ensure readiness.

Closing Notes

Recovering deleted files from virtual machine disks is possible if handled with care. Whether the issue is accidental deletion inside the guest OS, a corrupted VMDK, or even a missing virtual disk file, there are reliable methods to bring data back.

Act quickly, avoid overwriting the disk, and use the right tools for your specific situation. Prevention is always better than cure—set up backups, manage snapshots responsibly, and regularly test your disaster recovery plan to keep your virtual environments resilient.