Multi-step programming of heat-sensitive non-volatile memory (NVM) in processor-based systems, and related methods and systems are disclosed. To avoid relying on programmed instructions stored in heat-sensitive NVM during fabrication, wherein the programmed instructions can become corrupted during thermal packaging processes, the NVM is programmed in a multi-step programming process. In a first programming step, a boot loader comprising programming instructions is loaded into the NVM. The boot loader may be loaded into the NVM after the thermal processes during packaging are completed to avoid risking data corruption in the boot loader. Thereafter, the programmed image can be loaded quickly into a NV program memory over the peripheral interface using the boot loader to save programming time and associated costs, as opposed to loading the programmed image using lower transfer rate programming techniques. The processor can execute the program instructions to carry out tasks in the processor-based system.