Method and systems using stateful encryption for non-bypassable FPGA configuration including receiving, at an FPGA, FPGA-configuration data comprising a cryptographic state to initialize a cryptographic state of the FPGA, and decrypting, at the FPGA, the FPGA-configuration data, wherein decrypting the FPGA-configuration data yields at least a second cryptographic state and decrypted FPGA-configuration data. Embodiments can include receiving, at the FPGA, a challenge message, processing, at the FPGA, the challenge message to yield at least a third cryptographic state and a response, and transmitting the response from the FPGA.
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