The public sector constitutes a complex psycho-affective management system where leadership and autonomy are crucial for institutional effectiveness. The objective was to evaluate the differential influence of leadership management on autonomy and well-being in six departments of a municipal government in the state of Zacatecas, Mexico. A quantitative, correlational, and cross-sectional design was used with 235 public servants, employing Reference Guide III of NOM-035-STPS-2018 to identify psychosocial risk categories. The results, analyzed using Welch and Games-Howell tests, reveal significant differences (p < .001) according to the operational nature of each unit. Public Safety and Civil Protection present critical risks due to high demand and low control, while the Municipal DIF (System for Integral Family Development) stands out as a protective environment due to its positive leadership. A robust correla-tion was identified between poor leadership and lack of autonomy (rho = .701), in ad-dition to a widespread absence of recognition within the institution (p = .056). It is concluded that workplace well-being is conditioned by the command structure and the function performed, making it imperative to move towards an organizational culture that prioritizes occupational health to guarantee municipal operational sustainability.