The geothermal fumaroles present on Mt. Erebus, Antarctica, are home to numerous unique and possibly endemic bacteria. The isolated nature of Mt. Erebus provides an opportunity to closely examine how geothermal physico-chemistry drives microbial community composition and structure. This study aimed at determining the effect of physico-chemical drivers on microbial community composition and structure along extreme thermal and geochemical gradients at two sites on Mt. Erebus: Tramway Ridge and Western Crater. Microbial community structure and physico-chemical soil characteristics were assessed via metabarcoding (16S rRNA) and geochemistry (temperature, pH, total carbon (TC), total nitrogen (TN) and ICP-MS elemental analysis along a thermal gradient 10 °C–64 °C), which also defined a geochemical gradient. Diversity increased in alkaline soils suggesting pH to be the primary driver of microbial community structure across the gradients. Archaea dominated the microbial communities at Tramway Ridge compared to Western Crater, which was dominated by Bacteria. Western Crater has been sampled for the first time, widening the understanding of geothermal sites on Mt. Erebus. Organisms that were once considered cosmopolitan may not be as cosmopolitan as expected in Antarctica. These organisms may require specific niches that allow them to colonise new habitats. This study also showed that gathering more samples from Tramway Ridge has widened understanding of the changing environments that microbial communities on Mt. Erebus live in. The study provides a foundation on which to compare microbial and geochemical interactions across all geothermal sites within Victoria Land. This supports the effect of specific geothermal characteristics of the fumaroles in manipulating the microbial communities present.