The increase in the complexity of social and societal problems that even a large actor cannot solve alone has caused pressure on many sectors, organizations and entities making the need for collaboration to be more urgent. This is because collaboration enables merging financial resources, human resources, and expertise needed to tackle complex problems. However, the increased failure of collaborations requests greater consideration and investigation of the challenges in collaboration. The purpose of this study is to investigate the challenges in inter-organizational collaboration at management and employee level. To fulfill this purpose, inter-organizational collaboration towards open Skåne 2030 strategy was used as a case study. The empirical data showed that there are challenges in both the management and employee level in inter- organizational collaboration. Some of these challenges are similar for both levels while others are different. Further, the study also found that political influence is a major challenge in inter- organizational collaboration. The study makes a contribution to the adaptation of the Thomson and Perry (2006), model of collaboration process. The adapted model in the study serves to enlighten collaborators that challenges in inter-organizational collaboration are inter-linked.Keywords: Inter-organizational collaboration, collaboration process, management level, employee level.