Techniques to facilitate protecting control data used in an industrial automation environment are disclosed herein. In at least one implementation, an encryption key pair is generated for an industrial controller, wherein the encryption key pair comprises a public key and a private key. The private key is stored within a secure storage system of the industrial controller. Controller program content is then encrypted using the public key to generate encrypted controller content. The encrypted controller content is then provided to the industrial controller, and the industrial controller is configured to decrypt the encrypted controller content using the private key and execute the controller program content.