MacOS – Mac makes beeping sound every five minutes without pop up notification. Origin unknown

SoundBunny is a new app that I have just learned about. There is a free demo available which will work for 15 days (I think).

The app window will show you every app which is makes a sound. That might help you track it down.

You can also tell it to ignore apps which you have ruled out, which should help you narrow things down a but too.

I hope that helps.

(n.b. I am not related to this app except as a customer. The purpose of SoundBunny is to let you set the volume for each app, but I thought it might help with this as well.)

If a safe mode boot fails, you've got a damaged system.

Boot to recovery, internet recovery or external bootable media and reinstall the OS on top of all your existing apps and data. This preserves all data that's there.

If you suspect storage drive problems, you might check your last backup against another Mac to be sure it's up to date and restorable and possibly seek data recovery if you can't afford to lose the data before reinstalling the macOS.

I wouldn't do data recovery unless you have no backups and $300 or so for a professional service would be money well spent to safeguard your data. Most people recover from this with no data loss in about an hour or two after the reinstall starts, but I don't want you to not have the chance to back up before using the drive more if you suspect problems with the hardware and not just a third party extension causing lots of crashes.