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, Google Drive, Dropbox, OneDrive, pCloud, Box, Mega, plus dedicated connectors for self-hosted clouds — ownCloud, NextCloud, and SeaFile. S3/Azure/Google Cloud Storage are on the 2026 roadmap. Client-side encryption is planned but not shipped yet, so if that's critical today, Cyberduck's Cryptomator integration is the stronger choice.
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.