Background Socially Determined Diseases (SDDs) remain closely associated with health inequities and require coordinated responses from health systems, even in countries with universal healthcare coverage. In Brazil, the Brasil Saudavel Program (PBS) identified priority diseases and municipalities for elimination efforts, placing Municipal Health Plans (MHPs) at the centre of governance and policy implementation. Objective To analyse how and to what extent diseases prioritised by the PBS are incorporated into MHPs and translated into programmatic actions, considering municipal institutional capacity and service delivery organisation. Methods This descriptive documentary study analysed the MHPs of 175 municipalities prioritised by the PBS for the 2022-2025 planning cycle. Structured assessment instruments were developed based on the Programs National Guidelines to evaluate planning attributes, alignment with national priorities, and the operationalisation of disease-specific actions. Descriptive analyses were performed using absolute and relative frequencies. Pearsons chi-square test was used to assess associations between key planning attributes and regional differences. Results Although SDD-related goals were included in most plans, only 29.7% (n = 52) presented fully defined disease-specific targets, and 25.7% (n = 45) provided complete epidemiological information for all priority diseases. Dedicated funding was identified in 11.4% (n = 20) of municipalities, while fully structured awareness campaigns were described in only 4.0% (n = 7). Municipalities that incorporated epidemiological information into their plans were significantly more likely to describe structured prevention and control programmes than those without such information (76.7% versus 30.4%; {chi}2 = 29.8; p < 0.001). Regional differences were observed regarding the provision of disease-specific funding ({chi}2 = 12.0; p = 0.018), although planning profiles remained broadly similar across regions. Conclusions SDDs prioritised by the PBS are widely incorporated into MHPs at a declaratory level; however, their translation into structured programmatic actions remains limited. Weaknesses in financing, epidemiological intelligence, and operational planning constrain the implementation of national priorities. Strengthening municipal institutional capacity is essential to improve the operationalisation of health policies aimed at diseases shaped by social inequalities.