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If I want to make a VeraCrypt partition that's not an entire disk, I need to create a partition first and then let VeraCrypt overwrite it.

Does it matter what file system I give the partition before I let VeraCrypt take it over? Or will VeraCrypt completely overwrite the file system anyway?

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That's a very good question, and I couldn't find a clear answer in Veracrypt documentation.

So I did the experiment :)

FYI : I did this with Linux and GParted for initial partitioning, and of course Veracrypt for Linux for the next steps. I bet it should work similarly on any OS.

So :
I formatted by USB stick with two primary partitions. My aim is to encrypt the second and smaller one with Veracrypt. I put a dummy file in the bigger partition to later check that it was not deleted. I chose on purpose a file system not managed by Veracrypt, namely XFS : Initial state of partitions

Then I opened Veracrypt and launched the Volume creation wizard, making sure to create a volume within a partition / drive:
Veracrypt initial option

I went for a standard Veracrypt volume (i.e. not a hidden one) on my sdc2 partition (that I selected in the "Select Device" menu), with AES SHA-256 encryption protected by password only (my aim here wasn't to create a strong safe, just to test if initial file system can bother Veracrypt).
At final step, Veracrypt asked for a file system. XFS was of course not suggested. I selected FAT :
Veracrypt file system prompt

After encryption, I could successfully mount the encrypted volume, create a file on it, dismount the volume, re-mount it and retrieve my file. As expected, the file on my other bigger partition wasn't affected.

After that, the OS cannot guess what the partition is:
Final state of partitions

So, getting back to your question, it seems that the partition file system before encryption doesn't matter, Veracrypt will just re-format it.

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