Nanosatellites of CubeSat type due to, i.a., minimized costs of space missions, as well as the potential large application area, have become a significant part of the space economy sector recently. The opportunity to apply miniaturized microsystem (MEMS) tools in satellite space missions further accelerates both the space and the MEMS markets, which in the coming years are considered to become inseparable. As a response to the aforementioned perspectives, this paper presents a microfluidic mixer system for biological research to be conducted onboard CubeSat nanosatellites. As a high complexity of the space systems is not desired due to the need for failure-free and remotely controlled operation, the principal concept of the work was to design an entirely passive micromixer, based on lab-on-chip technologies. For the first time, the microfluidic mixer that uses inertial force generated by rocket engines during launch to the orbit is proposed to provide an appropriate mixing of liquid samples. Such a solution not only saves the space occupied by standard pumping systems, but also reduces the energy requirements, ultimately minimizing the number of battery modules and the whole CubeSat size. The structures of the microfluidic mixers were fabricated entirely out of biocompatible resins using MultiJet 3D printing technology. To verify the functionality of the passive mixing system, optical detection consisting of the array of blue LEDs and phototransistors was applied successfully. The performance of the device was tested utilizing an experimental rocket, as a part of the Spaceport America Cup 2023 competition.Graphical abstract