OPS-SAT is using Intel’s Cyclone V SoC in its experiment processing platform. Since the mission is entirely about experimentation, this SoC will be used for different purposes. Experiments range from FPGA based machine learning algorithms to Linux based communication applications. It is the need of the mission to safely reconfigure the SoC in space according to the experiment requirements. The extent of reconfiguration differs with each experiment, with some experiments requiring only FPGA configuration to be updated, while some others need changes in the operating system. This presentation will give an overview of the boot flow of Cyclone V and explain how we are making use of the flexibility it offers.