As a subclass of nanosatellites, CubeSats have changed the game’s rules in the scientific research industry and the development of new space technologies. The main success factors are their cost effectiveness, relative ease of production, and predictable life cycle. CubeSats are very important for training future engineers: bachelor’s and master’s students of universities. At the same time, using CubeSats is a cost-effective method of nearest space exploration and scientific work. However, many issues are related to efficient time-limited development, software and system-level quality assurance, maintenance, and software reuse. In order to increase the flexibility and reduce the complexity of CubeSat projects, this article proposes a “hybrid” development model that combines the strengths of two approaches: the agile-a-like model for software and the waterfall model for hardware. The paper proposes a new computing platform solution, “Falco SBC/CDHM”, based on Microchip (Atmel) ATSAMV71Q21 with improved performance. This type of platform emphasizes low-cost space hardware that can compete with space-grade platforms. The paper substantiates the architecture of onboard software based on microservices and containerization to break down complex software into relatively simple components that undergraduates and graduates can handle within their Master’s studies, and postgraduates can use for scientific space projects. The checking of the effectiveness of the microservice architecture and the new proposed platform was carried out experimentally, involving the time spent on executing three typical algorithms of different algorithmic complexities. Algorithms were implemented using native C (Bare-metal) and WASM3 on FreeRTOS containers on two platforms, and performance was measured on both “Falco” and “Pi Pico” by Raspberry. The experiment confirmed the feasibility of the complex application of the “hybrid” development model and microservices and container-based architecture. The proposed approach makes it possible to develop complex software in teams of inexperienced students, minimize risks, provide reusability, and thus increase the attractiveness of CubeSat student projects.