Methods and systems for protection of customer secrets in a secure reprogrammable system are disclosed, and may include controlling, via hardware logic and firmware, access to customer specific functions. The firmware may comprise trusted code, and may comprise boot code, stored in non-volatile memory, which may comprise read only memory, or a locked flash memory. A customer mode may be checked via the trusted code prior to allowing downloading of code written by a customer to the reprogrammable system. Access to customer specific functions may be restricted via commands from a trusted source. The hardware logic may be latched at startup in a disabled mode by the firmware, determined by the customer mode stored in a one time programmable memory. The customer mode may be re-checked utilizing the firmware, and may disallow the use of code other than trusted code in the reprogrammable system when the re-checking fails.