When comparing EncFS vs Cryptomator, the Slant community recommends Cryptomator for most people. In the question“What are the best free and open source cloud encryption tools?” Cryptomator is ranked 1st while EncFS is ranked 2nd.
Ranked in these QuestionsQuestion Ranking
Pro Encrypts on per-file basis
This makes it suitable for using with Dropbox or similar cloud storage platforms.
Works on Linux, OS X and experimentally on Windows.
Pro Configuration is stored in the working directory
The configuration for EncFS is in the form of a dotfile (.encfs6.xml) and it's stored in the working directory. This way you only have to remember the passphrase because all the other metadata is stored in the configuration file.
Pro Free and open source
Pro Transparent encryption
Pro AES individual file encryption
No accounts. No backdoors.
Pro Passphrase bruteforce protection (scrypt)
Pro Virtual hard drive file access
Drag and drop.
Pro Fast encryption and decryption
Available for Windows, Mac and Linux on desktop and iOS, Android for mobile.
Pro Works with any cloud platform
Works with any cloud-based services, including Dropbox and Google Drive.
Con Not up to speed with modern cryptography practices
From some audits in the past, EncFS has had some issues with being up-to-date as far as cryptography practices go. For example, it uses the same key for encryption and authentication or file holes not being authenticated.
Con Android version is paid
Con Bugs with deleting of files
Sometimes files cannot be deleted and there is no working solution/fix available yet
Con Current WebDAV is a buggy on Windows
The used WebDAV implemention shows wrong available capacity and has a limitation in the file size. The developers are aware of these problems and working on a better solution.
Con Compatible with Android versions 4.3 and up only
Con Slower speeds
Encypting speeds are slower then regular uploads, larger files particularly video files often cannot complete transfer without errors.
Con No camera upload functionality
Cannot automatically back up photos on mobile devices replacing the need for Google drive or iOS fully. User then has to go and either manually select photos for upload or use cloud service and then encrypt defeating the purpose on mobile clients.