Urbanisation is accelerating at unprecedented rates across the planet, causing rapid environmental change and posing a serious threat to global biodiversity. In order to minimise urbanisation’s impact on biodiversity we require an increased understanding about how organisms are adapting to city life. Many studies have provided evidence that animals can, and are, adopting a number of novel strategies to living within the city with growing evidence that many species are changing their diet under urban conditions. However, we still know very little about the extent to which modifications in diet influence the gastrointestinal microbiota community of urban organisms, which is critical to an individual’s health. Here, I will present results from isotopic analysis and gut microbiota community profiling across urban and non-urban populations of eastern water dragons to show how their diet, and in turn their microbiota, is adapting to city life.