Protocols and cloud support
This is one area where Cyberduck genuinely impresses. It supports a massive list of protocols and services: FTP, FTPS, SFTP, WebDAV, Amazon S3, Google Cloud Storage, Azure Blob, Backblaze B2, OpenStack Swift, Dropbox, Google Drive, OneDrive, and more. If you need to connect to obscure or enterprise cloud storage, Cyberduck probably supports it.
Cyberduck also has Cryptomator integration - client-side encryption for any cloud storage. This is a genuinely useful feature if you're security-conscious and want to encrypt files before they leave your machine.
FTPie's list is shorter but covers the services most people actually use: FTP, FTPS, SFTP, WebDAV, NAS shares over SMB, Google Drive, Dropbox, OneDrive, pCloud, Box, Mega, Koofr, OpenDrive, plus dedicated connectors for self-hosted clouds - ownCloud, NextCloud, and SeaFile. S3/Azure/Google Cloud Storage are on the 2026 roadmap. FTPie also ships its own client-side AES-256 file encryption: encrypt before upload, and decryption is free for anyone you share with. The difference from Cyberduck is the model - Cryptomator creates transparent encrypted vaults (a standard other apps can open too), while FTPie encrypts explicitly per file or folder in its own documented format.
Where FTPie differs is what you can do with those connections. It supports server-to-server transfers - moving files from SFTP to Google Drive, for instance, without downloading to your local machine first. Cyberduck doesn't do that; each transfer goes through your computer.