I’ve noticed a trend with errors on my NTFS backup drives so I started thinking about file systems and what might be the best file system to use for backups. So I’ve done some experiments to learn more. This is my personal experience from a lifetime of working with computers personally and professionally.
The Problems I see
The most common issue I see is were part of the file system will become inaccessible like the permissions have been corrupted. Or a file will not delete. Little stuff like that. It happen so often I added check disk commands to my backup scripts when I was on Windows. That solved the problem but it seem weird to me that this is a problem at all.
When I switched over to Linux I kept using NTFS and the problems would still happen but now I didn’t have an easy way to repair the file system.
So I started thinking about file systems and what options I had for my backup drives.
Other File System Options?
FAT
FAT is old but its still used a lot in small devices like my GoPro and Flipper Zero. It comes on a lot of USB and SD cards still. Anything 32GB and smaller and you will probably see FAT32 on them.
Its been around for a long time so we can say its stable. But it has 3 main draw backs
- It can’t support files over 4GB in size.
- It has no journaling so a sudden loss of power or disconnect can cause problems in the file system.
- Can be slow depending on file sizes.
Starting in Windows 10 there’s something called quick removal. It disables write caching on the device. You still don’t want to disconnect or lose power in the middle of writing a file but with this the file writes are done quick and cleanly finished narrowing the danger window.
I don’t know at this time if Linux or mac have anything like this but i’m in the habit of unmounting anyway to be on the safe side.
Personally I think FAT is fine on smaller drives and working with smaller files. Its stable and cross platform. As long as its disconnected properly I have not seen any issues with it on Windows or Linux. Most of the time if a USB drive fails for me it is hardware related and not a file system error.
So if your files are less then 4GB in size and your disk is on the small side then FAT32 is probably perfectly ok. But if your doing something like video editing then its not going to work for you.
exFAT
exFAT is an update to FAT32 so that it can support larger files and disk. It seems to work well. I had to repair it some but not nearly as much has I’ve repaired NTFS. I also think exFat has better support on Linux then NTFS so that could account for some of the better performance.
I formatted my video editing drive as exFAT and have been using it like that for over a year. One time Windows did tell me it needed to repair the file system when I hooked the drive up to a Windows box but other then that I’ve not had any issues.
Overall I like exFAT but just like FAT it lacks journaling so that could be an issue.
One thing about exFAT that is kind of annoying is the default cluster size is big. The theory behind this is to put less ware on flash memory. But if your working with small files you end up losing a lot of disk space. When I format exFAT I try to use the lowest cluster size of 4KB.
NTFS
NTFS is Microsoft’s main file system and a replacement from FAT32. Basically the whole Microsoft world runs on NTFS so it can’t be that bad can it?
But I work in IT and deal with big Windows file servers and I’ve seen issues pop up on NTFS drives. Several times a year some folder or file will not delete or have some other kind of random issue. Then I’ll have to take drives offline over the weekend to run disk repairs on them.
But at the same time I had not had much issues with the boot drive that the OS lives on. I noticed one day in some logs that Windows seems to do on the fly repairs of NTFS so maybe that’s why it works fine as a primary drive for windows? I can’t say for sure.
On my personal backup drives I just run robocopy or rsync once in a while. The drives set idle most of the time but I can say from my experience errors seem to creep up when I use NTFS.
EXT4
EXT4 is the default file system of Linux. This is Linux’s version of NTFS. Unfortunately getting Windows to read EXT4 is a pain and not very reliable. But as a backup drive for a Linux box it has never failed me yet. Out of all the file systems this one has been the most reliable for me. I know others will disagree but this is my experience with it.
For more low level info check out this cool post about EXT4. https://www.both.org/?p=3105
BTRFS
BTRFS is a new file system for Linux. It supports snapshots and software RAID. It seems like a really cool file system and is quickly becoming my favorite. I wrote a quick start guide to BTRFS if your interested. I ran it as a main file system on my laptop for a while and I’m currently running 2 disk on my desktop in a RAID 1 setup. I also made it the file system for my NAS.
I use it on a few backup drives and its always been good expect one time. I connected the drive to another computer. Then everything fail apart and I lost the data. Or at the very least, I didn’t know how to recover it.
In hindsight, I believe this was due to my own mistake when playing with the snapshot feature and a tool called snapper. The btrfs-progs commands for snapshots seems to be a lot more stable. So while I can’t suggest using it on your only backup drive for now I have a feeling that will change as I use it more.
Update 8-31-2025: After BTRFS saved me from some silent data corruption on my NAS last week I’m now a big fan. I noticed in scrubs that data kept having to be repaired on 1 disk. I thought the disk was going bad but it turns out it was the USB controller attached to the disk. Then it died.
I was able to mount the raid in read only mode with the good disk and make a new backup just in case. When I got a new part I was able to get it back up and running very easy using the btrfs-progs commands.
ZFS
ZFS is like BTRFS. It can do software raids and has checksums to try to self repair data. But it has two problems in my opinion.
First its owned by Oracle and they made it closed source so development has slowed significantly. It also slowed down adoption. Not a lot of systems support ZFS out of the box.
Second is when it fails it fails hard. I ran a NAS with ZFS once and at the time there were no recovery tools available. I had some kind of silent corruption and I lost everything on the NAS. Luckily I like to have lots of backups so nothing was lost permanently.
ReFS
This is a new Microsoft file system. I don’t really know anything about it other then it can’t be used to run Windows. Only for storage drives. Makes me wonder if there’s something to my theory above that NTFS has more issues on external drives.
My Rank For Best Cold Storage File System
For now i’m going to have to say BTRFS wins for me. It saved my butt and it’s able to detect if problems are creeping in. EXT4 is my second pick. I’ve never had major problems with it. But I’m also a Linux user. I can’t speak much about recovery tools because I never had to use any.
If I was forced to use Windows. Then I guess NTFS might be fine as long as you do disk checks once in a while. Their are tons of files out their that have lived on NTFS file systems for decades. so I can’t say its awful. Also their are lots of recovery tools for NTFS.
For compatibility I’d use exFAT on both Linux and Windows.
I guess looking at this now its not much of a surprise. Each OS’s own file system wins in their ecosystem. So really it all comes down to what OS your using and how much compatibility do you want.
Have More Then One Backup
The number one thing that matters more then anything else if you don’t ever want to lose anything is to have more then one backup. Maybe 1 backup drive and a cloud backup if you desire.
Right now I have 4 Backups all using their own file systems. EXT4, NTFS, exFAT, and BTFS. It might be a little overboard but i’m kind of OCD about backups. I’ve never lost anything and I want to keep it that way!
What are your experiences with different file systems? I would love to hear them in the comments below!
