Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of, and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome of a wild native non-model species – the eastern water dragon (Intellagama lesueurii). City dragons exhibit a more diverse gut microbiome than their native riparian counterparts and show gut microbial signatures of a high fat and plant rich diet. These results highlight the role that gut microbial plasticity plays in an animals’ response to human-altered landscapes.