A method for authenticating and deciphering an encrypted program file for execution by a secure element includes receiving the program file and a digital certificate that is associated with the program file from an external device. The method stores the program file and the associated certificate in a secure random access memory disposed in the secure element and hashes the program file to obtain a hash. The method authenticates the program file by comparing the obtained hash with a checksum that is stored in the certificate. Additionally, the method writes runtime configuration information stored in the certificate to corresponding configuration registers disposed in the secure element. The method further generates an encryption key using a seed value stored in the certificate and a unique identifier disposed in the secure element and deciphers the program file using the generated encryption key.