Shaded coffee plantations are of conservation value for many taxa, particularly for resident avifauna in the face of extensive landscape changes. Yet, little is known about the value of coffee plantations for amphibians because there are scant demographic data to index their value among species with different habitat preferences. We estimated the probability of occupancy of three frog species: Eleutherodactylus wightmanae, a forest species; E. brittoni, a grassland species; and E. antillensis, an open habitat species. Occupancy was estimated in sun and shaded plantations, and in secondary forest, in the west-central mountains of Puerto Rico. We also estimated the probability that a survey station was occupied by no individuals, one, or >1 individual, as a proxy of abundance. The aforementioned parameters, and local colonization and extinction probability, were modeled as a function of weather conditions (temperature, humidity) and vegetation cover at the sampling station (5 m) and contextual (100 m) scales. Encounter histories were obtained with passive acoustic recorders between February and July in 2015. Consistent with known habitat preferences, the highest occupancies were associated with secondary forests for E. wightmanae and sun plantations for E. brittoni. Occupancy probability for E. antillensis was similar across habitat types, indicating no aversion to shaded–forested habitats. Shaded plantations harbored moderate levels of occupancy for all species, indicating their potential value for multispecies conservation. Local colonization rates increased with forest cover for E. wightmanae, and with open habitats for E. brittoni and E. antillensis. Open habitats harbored a higher abundance of E. brittoni and E antillensis, but lower values for E. wightmanae. Sun and shaded plantations could provide quality habitat for Eleutherodactylus spp. if managed for features that promote local colonization and abundance.