When you’re using the zip CLI on your machine or a remote server and you need some extra security you can use the -e flag to encrypt a zip archive. Be sure to use a super long random password for this.
zip -e secure-files.zip ~/Documents/*.pdf
-e
--encrypt
Encrypt the contents of the zip archive using a password which is entered on
the terminal in response to a prompt (this will not be echoed; if standard
error is not a tty, zip will exit with an error). The password prompt is
repeated to save the user from typing errors.