Background: Collaborations between universities and industries are common to foster innovation in small and medium-sized enterprises. Participants of these collaborations face several challenges related to these collaborations. Universities and Industries work in different environments and value different priorities. Current literature shows that the challenges due to the organisational differences in these collaborations lead to the most significant challenges. Purpose: The purpose of this study is to explore and analyse how participants of UI collaborations perceive and manage organisational differences between universities and industries when the industry participant is a SME and the academic are students. We also aspire to discover and outline some specific characteristics of the organisational differences appearing in student-SME collaborations. Method: To fulfil the purpose, a qualitative study was conducted. The empirical data was collected in ten semi-structured interviews. Two projects of two master programmes at Jönköping University and experienced facilitators of university-industry collaborations were interviewed. The focus of the interviews was to get to know the participants' experience related to the organisational differences. Conclusion: The study's findings show how organisational differences in student-SME collaborations are perceived differently than in generic UI collaborations. Three elements were found as the main aspects influencing the perception of the organisational differences in student-SME projects: individual factors, perspective and collaborative factors. Finally, the findings show a positive contribution towards innovation in the SME participating in these projects.