MacOS Sequoia filling up with system data

I had the humongous System Data issue about a week ago (90MB of free space?!) and solved by 2 actions:

First deleting the offending cache* at ~/Library/Containers/com.apple.mediaanalysisd/Data/Library/Caches.

Next I upgraded to Sequoia 15.2, where apparently this cache over-filling is solved.

No problems now.

*in ~/Library/Containers/com.apple.mediaanalysisd one of the directories was humongous and filled 99.9% of free space. Go and check that directory in your ~/Library and by size it's immediately clear. Delete the oversize directory, and upgrade to MacOS 15.2 directly after that.

I could not upgrade to 15.2 prior to clearing this cache because, no free space...

I noticed this issue some weeks after upgrading to Sequoia, it probably appeared in Sequoia 15.1.

(the system had been creating a new mediaanalysisd cache file of 64MB probably every hour or so, without ever deleting the older ones. I saw an endless list of these 64MB files... On its own that sounds a small file, but in the end filled some hundreds of GB in that cache)

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!

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).

Not sure if this was resolved. Another suggestion :

I saw elsewhere that Disk Drill has a useful space analyzer in the free edition.

Load it up and look down left side menu for Clean Up option.

Then you can dig into where data is piling up.

One thing I noted while clean installing recently and copying large files across from old maching to new via Thunderbolt connection was huge files in a folder in the User/Library folder.

I don't recall exactly where it was located any more but looking online indicated it was files being created for the Handoff feature.

From what I read, using Command C and V to copy the files was causing the issue. Dragging would not. Not 100% sure why but I deleted the "cached" files and used darg and drop and it seemed to resolve the issue.

Maybe something to check out if you are a keyboard shortcut user and moving large files around rather than a drag and dropper.

My knowledge runs out there, but it could also only apply if between two separate entities - Mac to Mac or Mac to external hard drive for example.

I'm having this problem too! I spent an hour plus on the phone with Apple Tech Support last month. The fix we stumbled upon was to boot into Safe Mode. After booting into Safe Mode, my System Data shrunk from 365GB to 45GBs. I switched my Time Machine backup schedule from daily to weekly thinking that was the culprit, but I'm still having to boot into Safe Mode every 1-2 weeks to shrink my System Data.

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!

After updating my system, I always shutdown, then startup in Safe Mode. I had a fair amount, not super large amounts of System Data like some of you and after starting up in Safe Mode, then restarting it was significantly reduced. After updating to Mac OS 15.2 release candidate beta I had over 10 GB of Apple Intelligence in the Info button next to Mac OS in System Settings/Storage. This was reduced to 5.8 GB on my MacBook Pro M1 14 inch after starting in Safe Mode, then restarting normally. I would give it a try.

Have you used Activity Monitor to discover what is actually eating up the space?

Spotlight or more precisely mds_stores was writing huge amounts of almost 100 GB per day. Strangely they never physically appeared on my drive as though they were being deleted instantly.

Since completely disabling Spotlight in System Preferences the amount of "background" writes has dropped below 10 GB per day.

Had the same problem; fixed by going to Disk Utility, Show > Snapshots, deleting snapshots. These are disk images saving states of the system at different times to allow reversions, like an involuntary form of Time Machine.

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 .

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.