This work describes the onboard image processing pipeline that is designed to be used onboard a CubeSat with a Hyper Spectral (Imager/Image) (HSI), namely the HYPSO-1 satellite. While the system itself supports both the use of a Field Programmable Gate Array (FPGA) and CPUs for processing, this work focuses on the latter. A reference to the source code is also enclosed within the text. Some of the planned and developed modules are presented, along with the design choices needed to accommodate the computationally constrained system. The execution time of the pipeline on target hardware with representative hyperspectral data is also shown. The results indicate that the modular pipeline framework is suitable for deployment onboard HYPSO-1.