Inter-organizational collaboration among healthcare institutions is widely recognized to improve healthcare services. Because there is a research gap in examining the management barriers to inter-organizational collaboration in countries with less efficient healthcare systems and the reasons for non-implementation of innovations, the aim of this study was to identify key management barriers to inter-organizational collaboration in the preoperative treatment of patients with hip or knee osteoarthritis in Slovenia using a mixed-methods approach with key stakeholders. A cross-sectional study was conducted using multiple methods. An online survey (n = 135) and a multilevel qualitative approach were used, interviewing patients (n = 21), healthcare professionals, and other stakeholders (n = 42). The overall assessment of barriers affecting the integrated approach at the macro, meso, and micro levels revealed that macro-level factors were statistically significantly perceived as the major barriers, while micro-level factors were the minor barriers. There was no significant difference between public and private sector respondents in the barriers at the three levels. However, there were significant differences in the perceptions of different professional groups at the micro and meso levels, but not at the macro level. The analysis of the in-depth interviews confirmed the importance of macro-level barriers. A culture of noncooperation combined with “managerial indecision” prevails in the Slovenian healthcare system due to weak management support for inter-organizational collaboration, with managers and other key stakeholders failing to make urgent decisions due to a lack of autonomy. Interviewees commonly noted that one of the major barriers to inter-organizational collaboration was a lack of resources and staff, particularly of primary care physicians and nurses. In the preoperative treatment of patients with hip or knee osteoarthritis, the culture of non-collaboration and executive indecision are the major macro-level barriers to inter-organizational collaboration in Slovenia.