Patterned ground (PG) is one of the most evident expressions of cryogenic processes affecting periglacial soils, where macroscopic, repeated variations in soil morphology seem to be associated with small-scale edaphic and vegetation gradients, potentially influencing also microbial communities. While for high-latitude environments only few studies on PG microbiology are available, the alpine context, where PG features are rarer, is almost unexplored under this point of view. We followed a double approach, based on denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR), in order to investigate microbial community composition and abundance of phylogenetic markers and functional genes (bacterial and archaeal amoA) within single PG features and among different sites from four areas in the Western Italian Alps, characterized by different lithotypes. Bacterial, archaeal, and fungal community composition was quite homogeneous within single features, with more differences among samples collected from different lithologies. The abundance of phylogenetic and functional markers was uniform at different sites, except for the highest altitude one showing the lowest bacterial, archaeal, and ammonia-oxidizing archaea abundance. Nevertheless, at a small-scale level, a concentric distribution of microbial markers was described within single features, paralleling soil chemical property trends. These first results support the hypothesis that microbial ecology in alpine, periglacial ecosystems is driven by a complex series of environmental factors, such as lithology, altitude, and cryogenic activity, acting simultaneously on community shaping both in terms of diversity and abundance.