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BAMMsat-on-BEXUS is a student-led project aiming to design, manufacture, and fly a CubeSat-compatible payload on a stratospheric balloon. The payload – BAMMsat (Biology, Astrobiology, Medicine, and Materials Science on satellite) – is a modular CubeSat-format laboratory termed a bioCubeSat. The mission is realized under the bilateral REXUS/BEXUS programme run by the German Aerospace Center (DLR) and the Swedish National Space Agency (SNSA), with the Swedish payload share available to students through a European Space Agency (ESA) collaboration. The core objective of the prototype payload is to perform a technology demonstration of the core bioCubeSat technology, demonstrating its capability to support biological experiments in space. Additionally, the mission aims to validate pre-flight and flight operations, with a particular focus on biological operations. This will increase TRL for future bioCubeSat spaceflight with the goal to eventually enable better and cheaper biological, pharmaceutical, and materials science research in space environments. The BEXUS mission follows a typical space mission framework with reduced timeframe, therefore trade-offs prioritize commercial-off-the-shelf components and simple software using open-source solutions. The payload comprises a 2U pressurized laboratory payload (BAMMsat) and 1U avionics bus. The former contains experiment hardware including a Multi-Chamber Sample Disc, rotary mechanism, imager, the microfluidics system, active thermal control, and supporting avionics. The bus contains two flight computers, multiple custom avionics PCBs, and serves as the interface between BAMMsat and the BEXUS balloon gondola. The BAMMsat-on-BEXUS prototype will likely fly in October 2021. The prototype flight should prove that the system can perform varied microfluidics operations on multiple C. elegans samples, capture detailed imagery of the samples, provide general system housekeeping and communications, and provide life support for samples, including stable temperature and pressure despite operating within an extreme temperature and near-vacuum environment. The system and biological operations are designed to be fully automatic during flight, with some subsystems continually autonomously operating and others following sequenced events. Future work will aim for greater use of autonomous operations to reduce operating costs and enable more advanced system control, particularly for precise active thermal control and experiment sequencing. The next iteration of BAMMsat is targeting low Earth orbit missions, after further hardware upgrades and the inclusion of fluorescence microscopy and additional chemical sensors.