Background Challenges brought about by developments such as continuing market reforms and budget reductions have strained the relation between managers and physicians in hospitals. By applying neo-institutional theory, we research how intra-organizational dynamics between physicians and managers induce physicians to become entrepreneurs by starting a specialty clinic. In addition, we determine the nature of this change by analyzing the intra-organizational dynamics in both hospitals and clinics. Methods For our research, we interviewed a total of fifteen physicians and eight managers in four hospitals and twelve physicians and seven managers in twelve specialty clinics. Results We found evidence that in becoming entrepreneurs, physicians are influenced by intra-organizational dynamics, including power dependence, interest dissatisfaction, and value commitments, between physicians and managers as well as among physicians’ groups. The precise motivation for starting a new clinic can vary depending on the medical or business logic in which the entrepreneurs are embedded, but also the presence of an entrepreneurial nature or nurture. Finally we found that the entrepreneurial process of starting a specialty clinic is a process of sedimented change or hybridized professionalism in which elements of the business logic are added to the existing logic of medical professionalism, leading to a hybrid logic. Conclusions These findings have implications for policy at both the national and hospital level. Shared ownership and aligned incentives may provide the additional cement in which the developing entrepreneurial values are ‘glued’ to the central medical logic