A method, an integrated circuit and a system for implementing a secure chain of trust is disclosed. While executing secure boot code in a secure boot mode, less-secure boot code may be authenticated using a secret key. A secure key may also be calculated or generated during the secure boot mode. After control is turned over to the authenticated less-secure boot code, at least one application may be authenticated using the secure key. Once authenticated in the less-secure boot mode, the application may be executed by the programmable integrated circuit. In this manner, a secure chain of trust may be implemented for the programmable integrated circuit.