Governments are increasingly focusing their efforts on stimulating innovation within small and medium-sized enterprises (SMEs). As a result, university-industry-government collaboration is gaining importance among the agenda of policymakers to enable open innovation in SMEs. However, these inter-organisational relationships often fail to meet expectations, especially when projects are oriented to pre-competitive R&D. Nevertheless, the literature has not yet provided sufficient evidence of the challenges related to the participation of traditional SMEs (i.e., low- and medium-low tech SMEs) in this specific type of collaboration. We collected qualitative data to analyse longitudinally three pre-competitive projects, exploring the main challenges faced by traditional SMEs. We have bracketed the projects in four phases: initiation and planning phase, execution phase, closing phase, and monitoring and control phase. For each of these phases we have individuated firm- and project-level challenges, providing practical and theoretical insights for open innovation scholars. © 2021, The Author(s).