System-on-Chip (SoC) technology enables integrating all the functionality required to control and process science data delivered by space instruments in a single silicon chip (e.g., microprocessor + pro-grammable logic). This chapter discusses the implications of using this technology in deep-space exploration avionics, namely in the next generation of NASA science instruments that will be used to explore our Solar system. We present here our experience at the NASA Jet Propulsion Laboratory (JPL) using Xilinx Zynq SoC devices to implement the data processing of a Fourier transform spectrometer, namely the Compo-sitional InfraRed Imaging Spectrometer (CIRIS). Besides, we also discuss the different fault-tolerance techniques that have been implemented in the CIRIS controller SoC to deal with harsh radiation conditions prevailing in deep-space environments.