Looking at the published feature set of Cryptomator, it seems to be exclusively a file-based container. Whereas VeraCrypt additionally offers partition (including the system partition to protect the OS) and whole drive encryption.

Creating a quick Cryptomator vault, I noticed the key generation was automatic, VeraCrypt includes user-based input (mouse movement) as part of its key generation. In my opinion, done right / taken seriously, this offers better entropy.

VeraCrypt offers 15 encryption and 4 hash algorithms to choose from.

VeraCrypt also offers PIM (Personal Iterations Multiplier) modification / customization.

VeraCrypt can use a keyfile.

VeraCrypt offers hidden volumes for plausible deniability.

Looks like Cryptomator sets up a fairly deep directory structure, creating an encrypted file for each file added to the vault. This eludes to not only how many files are in the vault but also reveals size and date/time information. VeraCrypt’s container is just a single file of predetermined size, date/time stamp update is optional but off by default.

I believe these items make VeraCrypt more secure but at the cost of requiring the user to be more sophisticated.

I’m not a hater, Cryptomator’s ease of use may offer encryption to someone who may not otherwise leverage it and that is valuable.

Depending upon use case, performance may come into play which may be worth measuring.

The two programs are used for different things. VeraCrypt encrypts your disk, Cryptomator encrypts per file. It means the file/folder structure is not encrypted, but at the same time you can sync encrypted files over the cloud. VeraCrypt doesn’t encrypt files on the file system itself, it encrypts the whole file system.

Cryptomator is first and foremost meant to backup files on a cloud service, adding end-to-end encryption.

Vera Crypt is meant to encrypt a bunch of files, a disk partition or a system disk locally.

Both of them are needed, but their use case is completely different. You could use Vera Crypt to encrypt files before backing them up in the cloud, but it would be very inconvenient.

I think you can use Cryptomator for local encryption as well, but I’m not sure how it compares with Vera Crypt in that use.