House flies (Musca domestica) inhabit human-related environments on every continent. They are considered a nuisance as they are commonly found hovering around decaying matter, garbage, or feces as well as human food. They can vector several microorganisms on their exoskeleton or in their feces, including pathogenic microbes. The core microbiome of house flies has not yet been established and its widespread presence affords an opportunity to explore the influence of geography and habitat on its associated microbes. We sampled over 400 house flies from farms, homes, and hospitals in two geographically distinct countries: Belgium and Rwanda. The microbiome of each fly was studied using amplicon sequencing targeting bacteria and fungi. In addition to examining the internal microbiome of these insects, we also investigated the microbes found on the external surfaces of the flies. We found that the internal bacterial community of house flies is relatively stable regardless of geographic location or habitat but there are distinct differences in the internal fungal community. Moreover, bacterial and fungal communities associated with the external surface of flies is highly dependent on geographic location as well as habitat type. This is the first study to thoroughly explore the potential differences in the external microbiome and the fungal microbiome of house flies and demonstrating that the geographical location and habitat influences their composition.