I have a 1 TB internal drive (with APFS file system and FileVault enabled) I want to backup using Time Machine to an external USB hard drive. I want the backup itself encrypted so no one who has the hard drive can read/restore its content without a password.

Should I format the Time Machine partition as APFS or APFS (encrypted)? Should I select "Encrypt backups" option when creating the Time Machine or should I even do both?

I called Apple and they told me to do both but the call center agent did not really make the impression that he knows for sure.

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The simplest setup is to just connect any disk to the Mac and if you don't have Time Machine set up, you will be automatically prompted to use that drive and if it needs reformatting, that is explained. Then once the backups are set, if you are backing up an encrypted Mac to an unencrypted destination, Time Machine automatically prompts to encrypt the drive.

If you like doing things manually, here's more details and explanation that you want an HFS based drive to hold the backup whether you start from APFS or HFS.

For a time machine backup, you cannot use an external disk with APFS. You have to use Journaled HFS+. First, format your external disk as JHFS+ (Encrypted). After that, go to Settings > Time Machine and select your disk. If you have the option, select "Encrypt Backup". This way, your backup will be encrypted. So the answer to your question is neither of them. It is Journaled HFS+ (Encrypted). If you try to use APFS with Time Machine, you'll get the following warning:

Unsupported Filesystem Warning

Source: Apple - Backup disks you can use with Time Machine (APFS isn't mentioned at all)

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  • For a time machine backup, you cannot use a disk with APFS. Why is that? – Hedge Jul 19 '18 at 12:37
  • I don't know the exact reason. It's just like that. By the way, your internal disk's filesystem doesn't matter, only the external disk has to be JHFS+. – user255044 Jul 19 '18 at 12:39
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    @Hedge I've heard that it's because Time Machine v1 uses directory hard-links for incremental backups, which are not supported on APFS. (Source) – augurar Dec 23 '18 at 1:06

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