We analysed soil-borne microbial (bacterial, archaeal, and fungal) communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes located in Holocene raised beach and Tertiary volcanic stratigraphy. This is the first study to provide evidence for the crucial influence of landforms on small-scale structures and spatial heterogeneity of soil microbial communities.