The development of CubeSats has become an increasingly common trend among university student associations, primarily due to their relative affordability and simplicity compared to traditional satellite missions. These associations offer students the opportunity to engage in actual space missions, thereby providing valuable experience for their future careers in the space sector. Managing student-led space missions presents unique challenges, primarily due to the fluctuating involvement of students, whose participation is limited by academic commitments and usually shorter than the mission’s development timeline. This dynamic nature complicates knowledge transfer and decision-making, often altering the missions’ path and extending its duration. To address these challenges, an efficient project management approach is thus essential to navigate the complexities of such missions and achieve the desired outcomes. By utilising the case study of the student association EPFL Spacecraft Team and their 3U CubeSat mission CHESS (Constellation of High-Performance Exospheric Science Satellites), the paper identifies challenges within the association and establishes guidelines to overcome them, by interviewing present and past association members. These guidelines encompass various aspects, including team organisation, continuous reviews, in-orbit demonstrations, and open communication. By following these recommendations, the EPFL Spacecraft Team and also other student associations can enhance their project management practices and increase the likelihood of successful CubeSat missions.