Managed agroecosystems have been emphasized for their biodiversity, however, it remains unclear how biodiversity is affected by management practices over time. We assessed the seasonal response of the community of coffee-inhabiting mites to agroforestry management (simple-shade agroforests, complex-shade agroforests and abandoned coffee agroforests) in Ecuador. Species richness of coffee mites was negatively affected by management intensification, with more species in less-disturbed abandoned agroforests compared to simple-shade agroforests in the dry (but not in the rainy) season. Overall, the community of coffee-inhabiting mites varied seasonally, with more species and higher densities in the dry season than in the rainy season. In conclusion, our results show that the coffee mite community responded both to seasonal changes and to management of agroforests, and that vegetationally diverse habitats such as complex-shade and, in particular, abandoned coffee agroforests contribute to the conservation of mite diversity.