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Microbial communities were studied in redoximorphic microsites of highly heterogeneous Gleysol at a mm scale using 16S and 18S amplicon sequencing to demonstrate if the composition of soil microbes reflects the differences in ferric and ferrous micro‐sites. In both explored gley horizons with redoximorphic features (Bg2 and Cg), ferric mottles were significantly enriched with total P and Fe and depleted of O, Si, Al, K and Ca compared with the adjacent ferrous groundmass (SEM–EDS). Ferric mottles were determined as Fe oxide coatings and hypocoatings. In Bg2, both prokaryotic and micro‐eukaryotic communities differed significantly between mottles and groundmass in composition of operational taxonomic units (OTUs) and in proportions of phyla, reflecting heterogeneities in the soil properties there. Mottles in Bg2 were characterized by increased proportion of Proteobacteria, decreased proportion of Acidobacteriota among prokaryotes and by dominance of a single proteobacterial OTU from Anaplasmataceae compared to all other samples. The composition of micro‐eukaryotes showed an opposite trend, as micro‐eukaryotes of Bg2 groundmass were unique among the other horizons, while micro‐eukaryotes of Bg2 mottles had similar composition to neighbouring horizons. Microbial communities of adjacent samples were not more similar to each other than communities of randomly selected ones in Bg2 horizon. That suggests that at mm scale, the sample distance does not represent the driving factor of microbial community composition and that the adjacent samples differ rather due to physicochemical factors. The spatial organization of microbial communities revealed in Bg2 has not reappeared in similarly organized Cg horizon, probably due to other overriding factors. The differences revealed between Bg2 and Cg horizons, including granulometric composition, content of crystalline Fe, exchangeable Al, and organic carbon, as well as exposition to groundwater, were discussed as possible reasons of the distinct organization in Cg. The similarity of pro−/eukaryotic communities of adjacent and non‐adjacent couples suggests no distance decay pattern at a mm scale. The agreement between patchiness in soil properties and microbial communities was revealed for the first time and confirms the importance of microscale patterns in soil. [ABSTRACT FROM AUTHOR]