Species interactions are fundamental to ecological and evolutionary processes, shaping ecosystem dynamics and driving biodiversity. Among those, interactions between Diptera flies and amphibians are common in tropical areas, yet most aspects of their ecology and evolution are understudied. We systematically review the literature to examine the costs imposed by Diptera on amphibians and how these interactions have shaped the diverse strategies flies employ when interacting with these hosts. As flies can impose high costs on amphibians, we examine the array of defensive mechanisms they deploy against dipteran attacks, shedding light on the evolutionary arms race between them. We delve, for instance, into the eavesdropping behavior of some Diptera species, which use anuran calls as cues for host-seeking, and its potential impacts on frog communication systems. As flies can be disease vectors, we investigate pathogen transmission to amphibians as an indirect cost imposed by flies attacking them and examine the role of these interactions in disease dynamics. Finally, we address how human activities are currently impacting the long-established Diptera-amphibian interactions. We focus on potential disruptions caused by habitat alteration, the presence of invasive species, and climate change. By synthesizing existing knowledge of the costs imposed by flies on amphibians, we shed light on these groups of growing conservation concern given their current escalating extinction rates. Ultimately, our findings provide valuable insights into the intricacies of species interactions and underscore the urgent need for comprehensive studies mitigating the adverse effects of anthropogenic disturbances on these clades.