In Portugal, little is known about the work ability profiles of municipal workers and their changes during working life. In order to characterize and understand the changes in work ability among municipal workers, a prospective study was designed to begin in 2015 in the municipality of Sintra, in the surroundings of Lisbon, and to collect data every two years. The present paper aims at characterizing the changes in the work ability of those workers between 2015 and 2017 and to identify the main predictors. Data collection was based on a questionnaire that encompassed socio-demographic data, the Copenhagen Psychosocial Questionnaire II (COPSOQ II), the Nordic questionnaire adapted, and the Work Ability Index (WAI). In this two-year period, the work ability of municipal workers decreased and the main predictive factors were age, lower-back pain, negative health perception, the presence of burnout, and making manual efforts. Still, there were factors that act as positive predictors of an excellent work ability, such as having training in the previous two years, a good sense of community at work, and a favorable meaning of work. In summary, the intervention strategies in the work field should take into consideration the main predictors of work ability that are relevant for each organization.