How to fix Time Machine 'Preparing backup' issue when Spotlight indexing cannot be disabled?

As VikingOSX has already mentioned, Time Machine (TM) depends on Spotlight Indexing.

Regardless, when trying to ascertain a "tricky" TM backup issue, the best way to figure out where the culprit(s) is/are, is to review the macOS system logs.

On Catalina, this TM phase commonly stalls due to filesystem snapshot issues, permission errors, or a specific path that TM repeatedly fails to scan. These don’t always surface in the UI, but they do show up clearly in system logs.

If you're game into tackling the logs, here’s what I suggest you do next:

• Open Console.app and filter for `backupd` and `TimeMachine` while a backup is stuck in “Preparing.”
• Look specifically for repeating errors such as:
  • Failed to scan volume
  • Error enumerating files
  • snapshot invalid or com.apple.TimeMachine.localsnapshots
• If a specific path or folder is mentioned repeatedly, exclude that path from Time Machine (not Spotlight) and retry the backup.
• If the logs point to local snapshots, enter the following two commands in the Terminal app to both list all current local snapshots that are present, and to remove them. This safely clears problematic local snapshots, which is a very common cause of endless preparation on older Macs running Catalina.
  • tmutil listlocalsnapshots /
  • tmutil thinlocalsnapshots / 9999999999 4
• Finally, if logs show permission or ownership errors, a full-disk permission reset (via Recovery → Disk Utility → First Aid on the internal disk) is worth doing again after snapshot cleanup. At that point, if Time Machine still hangs with clean logs, the issue is almost always OS-level corruption, and recreating the Time Machine destination (erase + reselect) becomes the most reliable fix—even when the drive itself is healthy.

I'm throwing a lot at you, so if you need further assistance with any of these steps, please post back.

Since DriveDX is reporting the internal Apple SSD as S.M.A.R.T. FAILING with a Reallocated Sector Count = 13, that’s a major red flag. Apple SSDs normally don’t show that kind of behavior unless something is genuinely degrading at the NAND/controller level. In that situation, Time Machine failures aren’t the “problem” — they’re a symptom of the Mac struggling with storage reliability.

The Console messages (`backupd` sandbox denial for `user-preference-write com.apple.TimeMachine`, plus the TMHelperAgent process message) are likely secondary side effects of Time Machine services restarting/failing while the system is under storage stress. The TCC/AddressBook refusal is basically unrelated noise. If the internal SSD is unstable, you can see all sorts of weird backupd / permission / preference write failures because the OS can’t consistently complete reads/writes during the backup workflow.

What I strongly recommend that you perform if any of the drive's data is critical to you:

• Make a backup right now using a different method than Time Machine. I suggest using something like Carbon Copy Cloner or manually copying files to an external drive.
• It may still be good to double-check DriveDX's results. You can do so with native Apple tools, as follows:
  • Apple Menu → System Settings → General → Storage
  • System Information → Storage / NVMExpress
  • Look for anything indicating errors, failure, or inability to read SMART/NVMe status

Depending on how deep you want to go to verify your Mac's internal drive's health, there are a number of other things you can try. Just let me know.

If you want, tell me the exact Mac model + year + macOS version, and whether you’re seeing any other symptoms (beachballing, kernel panics, slow boots, random app crashes). I can help you confirm whether this looks like early-stage SSD failure vs filesystem corruption vs a false-positive SMART reading.

Ok, based on the images you provided, your iMac is equipped with the original Apple 1TB SSD option. Sorry, it wouldn't appear under NVMExpress as I had mentioned. That's not an issue so nothing to worry about there.

However, the issue remains that the internal Apple SSD is actively degrading and not trustworthy anymore. Reallocated sectors on an SSD generally means the controller has already started mapping out bad blocks, and the beachballing + Time Machine issues line up perfectly with the drive struggling to read/write reliably. At this point, the priority is data preservation first, and minimizing anything that forces lots of reads on that disk.

In practical terms: don’t attempt repairs, First Aid “fixes,” or OS reinstalls to the internal drive. Also, don’t let Time Machine keep hammering it. Your goal is to get to a stable boot volume ASAP (external is perfect), recover what matters, and then decide if the internal SSD replacement is worth the surgery ... for a 2013 iMac, it generally is not worth the cost nor effort.

What I recommend doing next (in order):

1. Stop Time Machine immediately. A failing SSD can get much worse when a backup is constantly forcing read activity and retries.
2. Get a good external SSD and boot you Mac from it. Look for SSDs that are, at least, 1TB in size. They can come with either USB-A or USB-C connectivity. For the latter, you would just need a USB-C to USB-A adapter in order to plug it into your Mac. Some good choices are: Samsung T7 Shield or the Samsung 870 EVO + USB 3.0 UASP enclosure. You would then ether install a "clean" copy of macOS Catalina onto this drive OR clone the current internal drive's content onto it.
3. Clone vs. migrate: If the iMac can still run for 30–60 mins without freezing, use Carbon Copy Cloner to clone internal → external once and be done. However, if it’s hanging, kernel panicking, or CCC hits tons of read errors: Do a fresh Catalina install to the external SSD, and then, use Migration Assistant to pull only what it can.
4. After the external boot is working, consider the internal drive “dead”.

A bad hdd (or ssd) on 2013 fusion hardware is more likely than not a problem

driveDX is a 10 min process from Google search download to screenshots (free trial)

if your hdd is indeed failing it could disappear and be unrecoverable if you keep messing around on it

i recommended using that time to clone while the drives may be functional

Because thats where I would start — to be sure I had a complete backup before going any further…

Please read the following user tip and restate your question/problem in detail: 

     Writing an Effective Apple Support Communities Question - Apple Community

What model and year is your Mac?

What size and type is your boot drive and how much free space do you have on it? If there's not enough room for a local snapshot you'll stall the process like you're experiencing.

What type of drive is the Time Machine drive and how is it formatted?

How much free space is on the TM drive.

I'd run Disk Utilities' Disk First Aid on the Time Machine drive. It will take a long time because of all of the hard links used by Time Machine.

Also boot into the Recovery volume (boot with the Command + R keys held down  - Intel Macs) or  (How to Boot a Silicon Mac into Recovery Mode) and run Disk Utilities' Disk First Aid on your boot drive. There may be a file that's damaged holding up the backup. Try repairing the boot drive first and then try Time Machine. If you get the same results repair the Time Machine drive.

Can you run DriveDX macOS and post drive health percentages and any failures on both internal drives (presuming you have a fusion ssd/hdd internal configuration)

maybe the entire report…

You haven't described your level of patience or how long you have waited for that Preparing to backup status. Depending on how long it has been since the last backup, this message may last for quite a long while and you would need to wait it out. I have seen these last for an hour or more before a backup resumed. However, this was a rare exception and ordinarily, to avoid this issue, I have Time Machine configured to backup hourly.

Time Machine and Spotlight work in concert with one another. Don't intercede.

What old toad said

I would immediately get a clone off that drive

i use Carbon Copy Cloner

Time Machine isn’t that complicated - something else is going on

how many gigabytes are on the source drive (the drive you want to back up)

how much free unused space is on your source drive

are the source and destination drives ssd or hdd

You say that you are "backing up the iMac and also an external hard drive". If I've understood this correctly then you are backing up the contents of the external drive to your Time Machine. If this is the case then spotlight will need to have indexed the external drive in order to do the backup. Spotlight keeps your Mac's hard drive indexed and up to date but if you have not been keeping the hard drive indexed or have turned off indexing then this might be why the "preparing" stage is taking so long.