Abstract Background The number of patients with long-term chronic diseases is increasing. These patients place a strain on health care systems and health care professionals (HCPs). Presently, we aimed to systematically review the literature on HCPs’ experiences working with patients with long-term chronic diseases such as type 2 diabetes, chronic obstructive pulmonary disease (COPD), and chronic kidney disease (CKD). Method A systematic search of papers published between 2002 and July 2019 was conducted in the Embase, AMED, PsycINFO, MEDLINE, CINAHL, and COCHRANE databases to identify studies reporting qualitative interviews addressing HCPs’ experiences working with adults with COPD, CKD or type 2 diabetes. An interdisciplinary research group were involved in all phases of the study. With the help of NVivo, extracts of each paper were coded, and codes were compared across papers and refined using translational analysis. Further codes were clustered in categories that in turn formed overarching themes. Results Our comprehensive search identified 4170 citations. Of these, 20 papers met our inclusion criteria. Regarding HCPs’ experiences working with patients with COPD, CKD, or type 2 diabetes, we developed 10 sub-categories that formed three overarching main themes of work experiences: 1) individualizing one’s professional approach within the clinical encounter; 2) managing one’s emotions over time; 3) working to maintain professionalism. Overall these three themes suggest that HCPs’ work is a complex balancing act depending on the interaction between patient and professional, reality and professional ideals, and contextual support and managing one’s own emotions. Conclusion Few qualitative studies highlighted HCPs’ general working experiences, as they mainly focused on the patients’ experiences or HCPs’ experiences of using particular clinical procedures. This study brings new insights about the complexity embedded in HCPs’ work in terms of weighing different, often contrasting aspects, in order to deliver appropriate practice. Acknowledging, discussing and supporting this complexity can empower HCPs to avoid burning out. Leaders, health organizations, and educational institutions have a particular responsibility to provide HCPs with thorough professional knowledge and systematic support. Trial registration PROSPERO number: CRD42019119052.