Seasonally dry tropical forests (SDTF) are among the most vulnerable ecosystems to chronic anthropogenic disturbances (CAD) such as agriculture, livestock and exploitation of wood and non-timber forest products which can negatively affect the local biota. We evaluated the influence of CAD and rainfall on the diversity of flesh flies (Diptera, Sarcophagidae) in the Brazilian Caatinga. We expected that the increase in CAD would negatively affect the specialist Sarcophagidae species and promote homogenisation of the assemblage. Specimens were collected using traps baited with fish, bovine spleen or human feces in six environments with different intensities of CAD—low, intermediate and high, based on land use and conservation status. We collected 29,810 specimens (3760 males, identified to 14 genera, 32 species). We observed a positive relationship between disturbance intensity and the abundance of synanthropic flies, mainly Tricharaea occidua. The diversity of common species and dominant species were affected only by CAD. There was also a marked substitution of species throughout the Caatinga environments (βSIM = 0.91), with few taxa (less than 50%) occurring indiscriminately in the areas under the three levels of impact. Chronic disturbances pose a constant threat to the conservation of flesh fly species. CAD act as a trigger for the homogenisation of Sarcophagidae assemblages, and magnify the dominance of synanthropic and generalist species. Empirical data on the effect of chronic disturbances can subsidize quantitative studies addressing local extinction. Our data strengthen the use of Sarcophagidae as biological indicators of anthropogenic action and can subsidize protocols for monitoring anthropogenic impacts in dry forests.