Bats can be parasitized by several arthropod groups, including ectoparasitic flies. The high host specificity is a common phenomenon between flies and bats. In recent years, more efforts have been employed to understand how environmental variables can influence richness and parasitic load (PL). However, many gaps still need to be filled to better understand this issue. We analyzed the PL of flies on bats sampled in three environments with different rain volume and vegetation types to verify if PL is correlated with rainfall and if there are differences in the PL on bats within and between environments. Overall, there was no correlation between rainfall and PL in the same environment, nor a difference between the three environments. When tested separately, Seba’s short-tailed bats (Carollia perspicillata (Linnaeus, 1758)) had a difference in prevalence of flies between environments and flat-faced fruit-eating bats (Artibeus planirostris (Spix, 1823)) had a greater abundance of flies in the rainy season in a semiarid area. There was no difference in PL between male and female bats. Our results suggest that bat–fly interactions are driven by several factors, not only by the amount of rainfall or vegetation, and that different host species may respond differently with no obvious general pattern.