Slow Copy Speeds for Large Numbers of Folders

Help Desktop App
1

Hello.
I’ve seen many help posts about slow copy speeds, but since I couldn’t find a solution, I’m posting here.

When I copy 10,000 folders, each containing a single image (this is the structure of the image management app I use), to a mounted vault, the speed drops significantly to about 5 MB/s (it’s about 70 MB/s in a Veracrypt container). Also, when I access the folder containing the 10,000 folders, there’s a long loading time of about 5 seconds, and performance becomes sluggish. On the other hand, large files of 2 GB each copy at high speed.

Is Cryptomator not suitable for handling large numbers of folders and files?

My device has an NVMe SSD, the volume type is set to WinFsp, and the only antivirus software I use is Windows Security.
I do not use the cloud; I only use local storage.

Thank you for reading.

2

Hi.

Did some testing.

Vault is on a HDD.

If I copy 10.000 folder with one 3 MB JPG file in each folder (29,2 GB) to the vault, it takes 6 minutes, 30 seconds. Thats an average of 76,7 MB/s

I also do not have a 5 second lag to list these 10k folders in the vault via the explorer.

Im afraid there’s something else that slows down your system.

3

Hi,

So, your copying large amounts of data to an external SSD from where? Is it going from your computers internal drive to an external drive?

Or, are you copying the files from an unencrypted folder to an encrypted folder on the same hard drive?

-–

I use and highy recommend an app called fastcopy windows only.

Fastcopy website

Windows file explorer is going to be a bottleneck for the transfer of 10,000 folders with a small file in each one.

Also windows robocopy is multi-threaded and a lot faster than using the regular copy command or File Explorer.

-–

Now you have:

10,000 folders

files are 3 MB each

If there is one file per folder, total data becomes:

10000 \times 3\ \mathrm{MB} = 30000\ \mathrm{MB} \approx 30\ \mathrm{GB}

So now you’re dealing with about 30 GB total, but with a very high file/folder count relative to data size.

That means the bottleneck shifts from raw SSD throughput to:

filesystem metadata

directory creation

small-file overhead

antivirus scanning

encryption setup per file

Scenario 1

Internal SSD → external SSD

Even though 30 GB is small for SSDs, 10,000 folders slows things down.

Typical real-world speeds:

100–400 MB/s effective throughput

not because SSDs are slow

because many small operations dominate

Estimated time:

roughly 2–10 minutes

depending on:

antivirus

USB speed

folder depth

whether files are fragmented

-–

Scenario 2

Same external SSD copy + encryption

This gets hit much harder now.

Why:

same SSD handling reads/writes

encryption overhead per small file

massive metadata churn

SSD random I/O instead of sequential

Effective speeds may drop to:

30–150 MB/s

Estimated time:

roughly 5–25 minutes

sometimes longer if encryption software handles each file separately

-–

Small files are the real killer

A single 30 GB file might copy in under a minute on a fast NVMe SSD.

But:

10,000 small files

inside 10,000 folders

can easily take 10× longer.

-–

Huge optimization trick

If possible:

1. Create one archive first using:

7-Zip

WinRAR

tar

2. Then encrypt/copy the archive.

This converts:

10,000 metadata operations into:

mostly sequential I/O

The speed difference can be enormous.

Example:

raw file copy: 15 minutes

archive then copy: 2–4 minutes

-–

Best tools for this workload

For many small files:

FastCopy is usually excellent

Robocopy with multithreading:

robocopy source dest /E /MT:32

rclone also performs well with parallel transfers

Windows Explorer is often noticeably slower with huge folder counts.