Field programmable gate arrays can be used as a shared programmable co-processor resource in a general purpose computing system. Components of an FPGA are isolated to protect the FPGA and data transferred between the FPGA and other components of the computer system. For example, data written by the FPGA to memory is encrypted, and is decrypted within the FPGA when read back from memory. Data transferred between the FPGA and other components such as the CPU or GPU, whether directly or through memory, can similarly be encrypted using cryptographic keys known to the communicating components. Transferred data also can be digitally signed by the FPGA or other component to provide authentication. Code for programming the FPGA can be encrypted and signed by the author, loaded into the FPGA in an encrypted state, and then decrypted and authenticated by the FPGA itself, before programming the FPGA with the code.