Abstract Introduction Although the concept of integrated care for non-communicable diseases was introduced at the primary level to move from disease-centered to patient-centered care, it has only been partially implemented in European countries. The aim of this study was to identify and compare identified facilitators and barriers to scale-up this concept between Slovenia and Belgium. Methods This was a qualitative study. Fifteen focus groups and fifty-one semi-structured interviews were conducted with stakeholders at the micro, meso and macro levels. In addition, data from two previously published studies were used for the analysis. Data collection and analysis was initially conducted at country level. Finally, the data was evaluated by a cross-country team to assess similarities and differences between countries. Results Four topics were identified in the study: patient-centered care, teamwork, coordination of care and task delegation. Despite the different contexts, true teamwork and patient-centered care are limited in both countries by hierarchies and a very heavily skewed medical approach. The organization of primary healthcare in Slovenia probably facilitates the coordination of care, which is not the case in Belgium. The financing and organization of primary practices in Belgium was identified as a barrier to the implementation of task delegation between health professionals. Conclusions This study allowed formulating some important concepts for future healthcare for non-communicable diseases at the level of primary healthcare. The results could provide useful insights for other countries with similar health systems.