Deploy your code and encrypted .env file to your server, and install the Dotenvx CLI there. Keep .env.keys on your local machine.
Find your private key with the keypair command.
$ dotenvx keypair
{"DOTENV_PUBLIC_KEY":"0220d830351410598be484f43a7b07097e09851f50426832876e8b5815a1752990","DOTENV_PRIVATE_KEY":"b37dbad0e00206f31486c4f44f8cc7abf2f1be96d5ba352eb791122b5e131bbf"}
Set it as DOTENV_PRIVATE_KEY on your production environment.
Run the same command on your server:
$ dotenvx run -- node index.js
⟐ injected env (2) from .env
Hello Secret
Dotenvx uses your private key to decrypt and inject your secrets just-in-time, but this time with the private key stored on your server.