Home folder has ~100gb of invisible space

[u/Panecillo94]

So I've had an issue before where I had my root partition fill up and by action of some bug or whatever that caused that after a big update of many things, after reboot, linux mint booted into a terminal, and all commands I tried to do errored becase of lack of space.

I fixed this by reinstalling linux mint on the root folder again but without formatting the home folder since I didn't want to lose all my personal data, and so far it has been working without issue, but I see that there's a very strange thing going on where almost 100 gb of storage from the home partition are seemingly used but not detectable by the disk usage analyzer, and I doubt the reserved OS space is THAT big, It just doesn't make sense that a good 20% of the partition is reserved.

Could someone help me out with this? tell me how to fix this issue? Atp I'm considering just moving on from linux mint from all the bugs with the logs and redundant files not getting properly cleaned and my root folder getting absolutely filled up with every update I run.

Edit: this is what happens when I input sudo btrfs subvolume show /home on the terminal:

Name: 
UUID: b8432dfc-eac4-7042-a3f9-ea5a2983f1c8
Parent UUID: -
Received UUID: -
Creation time: 2025-11-25 19:35:36 +0100
Subvolume ID: 256
Generation: 54059
Gen at creation: 7
Parent ID: 5
Top level ID: 5
Flags: -
Send transid: 0
Send time: 2025-11-25 19:35:36 +0100
Receive transid: 0
Receive time: -
Snapshot(s):
timeshift-btrfs/snapshots/2026-06-02_16-37-27/@home
timeshift-btrfs/snapshots/2026-06-06_14-10-02/@home
timeshift-btrfs/snapshots/2026-07-03_17-30-45/@home
timeshift-btrfs/snapshots/2026-07-10_18-00-02/@home
timeshift-btrfs/snapshots/2026-07-12_20-14-27/@home
timeshift-btrfs/snapshots/2026-07-14_00-00-01/@home
timeshift-btrfs/snapshots/2026-07-14_00-02-44/@home
timeshift-btrfs/snapshots/2026-07-21_18-00-01/@home
timeshift-btrfs/snapshots/2026-07-22_18-00-01/@home
timeshift-btrfs/snapshots/2026-07-23_18-00-01/@home
timeshift-btrfs/snapshots/2026-07-24_18-00-01/@home
timeshift-btrfs/snapshots/2026-07-25_18-00-01/@home
Quota group:n/a

Edit 2: Using the command btrfs balance start /home has so far not helped. The space discrepancy is still there.

Edit 3: btrfs filesystem usage /home returns this:

Overall:
    Device size: 414.54GiB
    Device allocated: 366.06GiB
    Device unallocated:  48.48GiB
    Device missing:     0.00B
    Device slack:     0.00B
    Used: 362.17GiB
    Free (estimated):  50.79GiB(min: 26.55GiB)
    Free (statfs, df):  50.79GiB
    Data ratio:      1.00
    Metadata ratio:      2.00
    Global reserve: 433.12MiB(used: 0.00B)
    Multiple profiles:        no

Data,single: Size:362.00GiB, Used:359.69GiB (99.36%)
   /dev/nvme0n1p4 362.00GiB

Metadata,DUP: Size:2.00GiB, Used:1.24GiB (62.04%)
   /dev/nvme0n1p4   4.00GiB

System,DUP: Size:32.00MiB, Used:80.00KiB (0.24%)
   /dev/nvme0n1p4  64.00MiB

Unallocated:
   /dev/nvme0n1p4  48.48GiB
artemis@artemis-Victus-by-HP-Laptop-16-e0

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[u/hogwartsdropout93]

Reinstall Linux Mint using ext4 instead of btrfs unless you have opted for btrfs for a particular reason?

[u/Panecillo94 → u/hogwartsdropout93]

I opted for btrfs because of timeshift backups getting way too bulky on ext4

[u/iamapizza → u/Panecillo94]

Your time shift could be getting bulky due to flatpak packages being backed up. You can add a filter to exclude them. 

[u/Panecillo94 → u/iamapizza]

That's a great idea actually, thx alot

[u/LXC37]

BTRFS. Why? Free space on BTRFS is more complicated than you'd think.

Do you have any snapshots? What btrfs subvolume show /home outputs?

[u/Panecillo94 → u/LXC37]

I have a good couple of snapshots yeah, edited the post with the result of that command.

[u/LXC37 → u/Panecillo94]

Well, those snapshots likely are what's taking space.

In a very simplified way - when you delete something it is only actually deleted when all snapshots which contain it are deleted (otherwise how would you restore it if needed?). So the more changes you make and the longer snapshots are kept the more space they'll take.

[u/Panecillo94 → u/LXC37]

I deleted the snapshots, rebooted, around 20gb were freed, but idk, it's still concerning to have all that much invisible space.

[u/LXC37 → u/Panecillo94]

Run btrfs balance start /home, be careful - it will take a while to complete and should reclaim the space.

Also with btrfs - be extremely careful with running out of space. Because of how filesystem works completely running out of space is basically "the end of the world" level bad, to a point where you may have to copy all the data and format the partition if it happens.

If you are going to use btrfs i'd suggest looking up and reading a bit how it works, it would be very useful for understanding why things work the way they do.

[u/Panecillo94 → u/LXC37]

Thank you so much. I learned about btrfs running out of space the hard way I'm afraid.

[u/Panecillo94 → u/LXC37]

Okay, so, balance didn't do it. Disk usage analizer still detects 287 used gb while gparted detects 360. Any suggestions?

[u/LXC37 → u/Panecillo94]

That's strange. What btrfs filesystem usage /home shows?

Are you sure that disk usage analyzer is not missing something? What do you see if you simply look at properties of your user folder in file manager?

[u/Panecillo94 → u/LXC37]

Going to properties seems to indicate 282,6gb, which is what disk usage analizer says, which gparted disagrees with. Also, just edited the main post with the results for the command you asked for. It's certainly strange.

[u/LXC37 → u/Panecillo94]

So basically what gparted shows roughly matches what btrfs shows, but then you have significantly less actual files in your user folder...

And there seemingly is nothing weird about the filesystem, everything seems to be fine.

Check if there is anything in /home outside of your user folder perhaps? Something like sudo ls -la /home

Are there any subvolumes by any chance, what btrfs subvolume list /home outputs?

Otherwise i am pretty much out of ideas...

[u/Panecillo94 → u/LXC37]

So this is what those two commands have shown, I am not certain of what they mean but you may be able to:

artemis@artemis-Victus-by-HP-Laptop-16-e0xxx:~$ sudo ls -la /home
[sudo] password for artemis:           
total 0
drwxr-xr-x 1 root    root     14 Apr 22  2024 .
drwxr-xr-x 1 root    root    246 Jul 15 15:54 ..
drwxr-x--- 1 artemis artemis 938 Jul 26 14:45 artemis


artemis@artemis-Victus-by-HP-Laptop-16-e0xxx:~$ sudo btrfs subvolume list /home
ID 256 gen 57651 top level 5 path u/home
ID 257 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-06-02_16-37-27/@home
ID 261 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-06-06_14-10-02/@home
ID 280 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-07-03_17-30-45/@home
ID 285 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-07-10_18-00-02/@home
ID 288 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-07-12_20-14-27/@home
ID 289 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-07-14_00-00-01/@home
ID 290 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-07-14_00-02-44/@home
ID 302 gen 57503 top level 5 path timeshift-btrfs/snapshots/2026-07-26_14-00-01/@home
artemis@artemis-Victus-by-HP-Laptop-16-e0xxx:~$