MacOS Sequoia filling up with system data

I also have a lot of System Data after upgrading to Sequoia. It's only 60 GB, but that's 1/4 of my 256 storage capacity. Is this a glitch in the system? Is any of this data non-essential and purgeable?

First of all, thank you SO much for the extremely quick response!

I'd say about 10 minutes after I posted my previous message - and while I was using Disk Inventory X to scan for any hidden huge folders - my Mac suddenly decided it felt 200gb lighter..

I'm not sure if the actual folder scanning did anything or it just randomly felt like unclogging the drain, but I'm not sitting comfortably at 'only' 200gb system data...

I stumbled across a fix for my system data problem that you all seem to be having too.

The crazy thing is that I didn’t do anything other than locate the folder in the library that stored the nearly 1 TB of system data…and it’s somehow all good now. 

Here is exactly what I did:

-Open finder -> Go -> Library -> View -> View Options -> “Calculate All Sizes” option -> Sort the Library by Size.

When I viewed the Library sorted by size, and when calculating all sizes was turned on (which shows the size of the folder and all subfolders in it), then it showed the largest folder clocking in at more than 1 TB total. That folder is the “Group Containers” folder. When I double clicked this folder to check out what’s in there, it became clear immediately that I didn’t understand what I was looking at, so I didn’t touch anything in there and I went back. 

I don’t understand what happened next, but the Group Containers folder immediately went down from being more than a TB to about 82 GB. 

Then when I went to look at my storage info in system settings, it showed the system data folder had shrunk just as much as the Group Containers folder had just shrunk. I don’t get it, but it’s fixed and that’s how it happened.

Credit to this YouTube video that I didn’t even finish watching because it fixed itself at basically step 0 of the video.

https://youtu.be/9P4oqri4dYc?si=_o81P9CmOg5sUYmY

Hopefully it works for you all too!

edit: I have a MacBook Pro M4 (my first Mac computer ever).

I had been struggling with this issue for a long time. No matter what I tried—clearing cache, deleting unnecessary files, following every trick on YouTube and forums—the System Data just wouldn’t shrink. Sure, I managed to free up a little space here and there, but the core problem remained.

It felt like my Mac was hoarding space for no reason. 120GB of precious storage was stuck under “System Data,” and I couldn’t figure out why. I was running out of options, so I turned to AI and asked for every possible solution.

Then, AI suggested something I hadn't seen before:

Run this command in Terminal:

sudo mdutil -a -i off

I had nothing to lose, so I ran it… and BOOM! My used storage dropped from 80% to 40% in an instant. That stubborn 120GB of system data shrank to just 35GB!

So, what does this command do?

It disables Spotlight indexing across all drives. macOS uses Spotlight to keep track of your files, but over time, its database can grow ridiculously large. By turning it off, I freed up a massive chunk of storage. If you don’t rely heavily on Spotlight search, this is a game-changer.

If you ever want to turn it back on, just run:

sudo mdutil -a -i on

For me, this was the magical fix I had been looking for. Hope it helps you too! 🚀

Been fighting this issue for awhile. here's what worked for me:

• Putting the hard drive in Spotlight's do not analyze list cut the amount of System Data in half
• I was following TechSiren's YouTube video (https://www.youtube.com/watch?v=9P4oqri4dYc) and when I clicked "calculate all sizes" the amount of System Data started dropping dramatically. I'm currently down to 120 gb.

hope this is helpful to someone!

Edit: as I was typing this I turned spotlight back on with most of the check boxes unchecked. System data dropped from 120 GB to ~80 GB!

Has this been answered? I have the same issue

A few days ago I noticed that the disc usage had jumped from approx. 50% to 90% (Mac M1 Sequoia, 512 GB SSD). The system data suddenly occupies more than 200GB. When analysing under root, I found that all non-linked root folders (/Applications, /Users etc.) are also present in the /System/Volumes/Data folder with the same inode numbers. Linked or mirrored - no idea. If mirrored, this would mean that since Sequoia only about 50% of the disc is effectively available... If linked, all the disk (usage) utilities should be updated a.s.a.p...

Until now, common tools for disc usage (e.g. DaisyDisk, df, du) calculate everything there twice. 

Scanned with du in "/System/Volumes/Data":

iMac:/System/Volumes/Data$ du -m -d 1 -x 2>/dev/null

...

11498 ./Library

2295 ./System

3339 ./private

196761 ./Users

20745 ./Applications

33626 ./opt

...

Total: 272983 .

Scanned with du in "/":

iMac:/$ du -m -d 1 -x 2>/dev/null

...

11498 ./Library

284634 ./System (with ./Volumes/Data/...)

3340 ./private

196766 ./Users

20745 ./Applications

33626 ./opt

...

Total: 551301 .

I've been just going through the same (630GB!) and this thread been very helpful. The suggestion to navigate through your folders changing view options to 'calculate all sizes' is a good one.

In my case, I've found the system data storage figure to be pretty legit as the amount appears to include:

• iCloud data (~350GB) that I keep locally. Strange that Apple do that rather than include it under iCloud which you'd think would be less opaque but anyway.

• Hidden files/folders. E.g. I had downloaded a distilled version of deepseek-r1 that was another 230GB... but it was spread across some hidden .git folders so wasn't showing up under Documents. Hidden files/folders seem also to be included in system data.

This command in terminal will list the top N largest files including hidden files - change the last number to the top N you want to see. It's a better way to find big files:

find . -type f -print0 | xargs -0 du -h | sort -rh | head -n 10

• One poster also mentioned the Library/Containers folder as being massive. Just bear in mind this can contain files that report as being big but aren't e.g. if you have things like Docker installed this can contain 'placeholders' such as the Docker.raw image which can be report >1TB but isn't and should be left alone (or in this case you can modify in docker setting).

This is a common issue and no easy way to delete. The system data grows with time. One effective way is to delete the app caches.

With the help of Apple support and many hours of troubleshooting and diagnostics we were able to identify the problem and regain the disk space from System Data. The culprit in my case was Carbon Copy Cloner a backup and disk cloning utility of which a snapshot was occupying 416GB of disk space when it should not have been.

To get rid of this I booted into recovery mode while holding "Command & R" while starting the computer

Ran Disk Utility and selected View > Show APFS Snapshots > selected the snapshot and deleted it.

Upon restart my disk usage was somewhat back to normal. I have a 1TB drive and used space was 444GB but Available space said 998GB. Clearly there was some lingering calculation challenges but Apple said that would sort itself out in time or would update correctly if an OS update was done.

Sure enough after I updated to Sequoia 15.3.2 everything appears to be back to normal.

Fingers crossed that things remain that way and hopefully this may help some of you also experiencing this issue!

With the help of Apple support and many hours of troubleshooting and diagnostics we were able to identify the problem and regain the disk space from System Data. The culprit in my case was Carbon Copy Cloner a backup and disk cloning utility of which a snapshot was occupying 416GB of disk space when it should not have been.

To get rid of this I booted into recovery mode while holding "Command & R" while starting the computer

Ran Disk Utility and selected View > Show APFS Snapshots > selected the snapshot and deleted it.

Upon restart my disk usage was somewhat back to normal. I have a 1TB drive and used space was 444GB but Available space said 998GB. Clearly there was some lingering calculation challenges but Apple said that would sort itself out in time or would update correctly if an OS update was done.

Sure enough after I updated to Sequoia 15.3.2 everything appears to be back to normal.

Fingers crossed that things remain that way and hopefully this may help some of you also experiencing this issue!

Nothing is what it seems at first - With the standalone version of DaisyDisk I got a deeper insight into the structure of the system data on the disk. It turned out that the remote backup software I use, 'ChronoSync', necessarily creates or uses an APFS snapshot volume. The size of this third party snapshot corresponds to the size of the data to be synchronized and is approx. 120 GB in my case. The rest of the system data is occupied by macOS. E.g. by TimeMachine snapshots and other areas that are not accessible to the user. The output of the command line program 'du' was particularly confusing for me.