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Abstract Background Patient-centeredness and therapeutic relationship are widely explored as a means to address the challenge of chronic disease and multi-morbidity management, however research focusing on the perspective of doctors is still rare. In this study, we aimed to explore the impact of the patient’s chronic disease(s) on their healthcare provider. Methods A qualitative approach was taken using semi-structured interviews with general practitioners working in outpatient clinics either in individual practices or in a hospital setting in Geneva, Switzerland. Codes were developed through an iterative process and using grounded theory an inductive coding scheme was performed to identify the key themes. Throughout the analysis process the research team reviewed the analysis and refined the coding scheme. Results Twenty interviews, 10 in each practice type, allowed for saturation to be reached. The following themes relevant to the impact of managing chronic diseases emerge around the issue of feeling powerless as a doctor; facing the patient’s socio-economic context; guidelines versus the reality of the patient; time; and taking on the patient’s burden. Primary care practitioners face an emotional burden linked with their powerlessness and work conditions, but also with the empathetic bond with their patients and their circumstances. Doctors seem poorly prepared for this emotional strain. The health system is also not facilitating this with time constraints and guidelines unsuitable for the patient’s reality. Conclusions Chronic disease and multi-morbidity management is a challenge for healthcare providers. This has its roots in patient characteristics, the overall health system and healthcare providers themselves. Structural changes need to be implemented at different levels: medical education; health systems; adapted guidelines; leading to an overall environment that favors the development of the therapeutic relationship.