We present the data acquisition and control software for the operation of the Mini-Extreme Universe Space Observatory (EUSO), a space-based fluorescence telescope for the observation of extensive air showers and atmospheric phenomena. This framework has been extensively tested alongside the development of Mini-EUSO and was finalized ahead of the successful launch of the instrument to the ISS on August 22, 2019. The data acquisition, housekeeping, and subsystem control is achieved using custom-designed front-end electronics based on a Xilinx Zynq XC7Z030 chip interfaced with a PCIe/104 CPU module via the integrated Zynq processing system. The instrument control interface is handled using an object-oriented C++ design, which can be run both autonomously and interactively as required. Although developed for Mini-EUSO, the modular design of both the software and hardware can easily be scaled up to larger instrument designs and adapted to different subsystem and communication requirements. As such, this framework will also be used in the upgrade of the EUSO-TA instrument and potentially for the next EUSO-SPB2 NASA Balloon flight. The software and firmware presented are open source and released with detailed and integrated documentation.