<p>To analyze Primary Health Care physicians’ perceptions of the challenges involved in managing Chagas disease in areas with higher and lower endemicity. This qualitative study was conducted in three municipalities in the state of Minas Gerais, Brazil. Four focus groups involving 27 physicians were carried out. Discussions were guided by a semi-structured script based on the Clinical Protocol and Therapeutic Guidelines for Chagas Disease, audio-recorded, transcribed verbatim, and analyzed using thematic content analysis according to Bardin, with independent double coding. The findings revealed gaps in professional training, predominance of theoretical teaching, lack of continuing education activities, and limited knowledge of the Clinical Protocol and Therapeutic Guidelines. Low clinical suspicion, uncertainties regarding notification of chronic Chagas disease, and the association of antiparasitic treatment primarily with the acute phase were also identified. In municipalities with higher endemicity, low rates of serological testing requests were observed, whereas in the municipality with lower endemicity, Chagas disease was less frequently considered among diagnostic hypotheses. These findings indicate that educational, clinical, and organizational weaknesses contribute to maintaining the invisibility of Chagas disease within Primary Health Care and that higher local endemicity alone does not ensure its incorporation into routine work processes. The results highlight the importance of continuing education, stronger integration between Primary Health Care and Health Surveillance, and the incorporation of clinical guidelines to enhance the capacity of Primary Health Care services to recognize, diagnose, and provide follow-up care for individuals affected by Chagas disease.</p>