Embedded systems are becoming nearly ubiquitous, found in a plurality of devices ranging from everyday cars and dishwashers to sophisticated spy satellites and remote sensing equipment. As the applications for embedded systems increase in number and diversity and continue to pervade our lives, a need arises to secure these systems. Whether the need arises from a desire to protect personal, proprietary, sensitive, or classified information, the security of the embedded system seeks to maintain the confidentiality and integrity of data contained within the system. Research into securing embedded systems is in its nascent stages. The generally accepted methodology of securing embedded systems involves techniques that either modify an embedded system's processor or entail custom ASIC hardware. This thesis presents a novel embedded system architecture for secure software processing that does not involve processor modification, but rather processor augmentation to ensure the confidentiality and integrity of information contained within the embedded system. Specifically, configurable logic placed at the processor periphery provides just-in-time cryptographic transformation of instructions, data, and I/O of a running embedded application. In addition to presenting the embedded secure software platform, this thesis provides a characterization of the data protection architecture of the platform.