TL;DR: My macOS System Data was massively inflated because the Spotlight index (/System/Volumes/Data/.Spotlight-V100) had grown to ~174 GB. Rebuilding the Spotlight index with mdutil brought System Data down and freed a lot of space.

macOS “System Data” extremely large — what I did (Spotlight reindex fixed it)

I ran into the classic macOS storage issue where System Data becomes absurdly large and it feels like a huge chunk of disk space is “missing”. I’m sharing what worked for me in case it helps others.

Before: ~260 GB System Data, ~30 GB free space
After: ~83 GB System Data, ~210 GB free space

Context (because I’m not a power user)

• I first tried a few “cleanup” apps. They only removed around ~5 GB, which didn’t really change anything.
• Also tried Clear cache on Mac by going to the
  • /Library/Caches/
  • /System/Library/Caches/
  • But that did't help a lot...
• I’m not a programmer and I don’t know much about filesystem / APFS internals.
• It was honestly frustrating.

I then started troubleshooting with help from ChatGPT. The original conversation was much longer than what I’m posting here; this is a summary I kept in Evernote, so a couple of small details might be missing. But I think it contains enough concrete steps for people to try.

Key idea

macOS storage reporting can be confusing because APFS uses copy‑on‑write, shared blocks, and “purgeable” space. That means you can’t always find a single obvious folder matching the System Data number.

In my case, the “missing” space turned out to be a massive Spotlight index.

What I checked (in order)

1) Confirm the Storage categories in macOS

Go to:
System Settings → General → Storage

Wait a minute or two for the categories to fully refresh, then note:

• System Data size
• Free space

2) Rule out “deleted but still open” files

Sometimes a process keeps a deleted file open, so the space is still used but tools like du won’t see it.

Run:

sudo lsof +L1

Look for lines containing (deleted) with unusually large sizes.

Result for me: no huge deleted files were being held open.

3) Check Spotlight’s database size

This is where the real issue showed up.

Run:

sudo du -sh /System/Volumes/Data/.Spotlight-V100

In my case it was around ~174 GB.

(Inside it, most of the size was in Store-V2.)

4) Check Spotlight indexing status (optional)

mdutil -s /
mdutil -s /System/Volumes/Data

5) The safe fix: rebuild the Spotlight index

Important:

• Do not manually delete system directories with rm -rf.
• Let macOS rebuild the index.

Run:

sudo mdutil -E /System/Volumes/Data

Then wait (this can take a while).

6) Verify it’s shrinking / Storage improves

Re-check Spotlight size:

sudo du -sh /System/Volumes/Data/.Spotlight-V100

And revisit:
System Settings → General → Storage

In my case, after reindexing, System Data dropped massively and free space returned.

Notes / cautions

• During reindexing, CPU/SSD activity can be higher and storage numbers can fluctuate temporarily.
• If you have huge cloud-sync folders (photos, design assets, etc.), Spotlight can balloon.

Quick checklist

1. Storage screen: note System Data + free space.
2. sudo lsof +L1 (check for huge “(deleted)” files).
3. sudo du -sh /System/Volumes/Data/.Spotlight-V100 (is it massive?).
4. sudo mdutil -E /System/Volumes/Data (rebuild index).
5. Re-check Spotlight size + Storage screen.

If anyone has other root causes for System Data spikes (besides Spotlight), feel free to add them.

Success.