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• The type of soil cover (mosses vs. biocrusts) affects subjacent soils differently. • Higher abundance of microbial biomass but lower microbial activity under biocrusts. • Lower abundance of all compound groups of organic matter under mosses. • Moss-specific traits matter for composition of SOM and microbial communities. • Future changes in soil cover type abundance may alter soil functioning. Bryophytes and biological soil crusts (biocrusts) are the two major biological soil cover types of maritime Antarctica and play a crucial role for key ecosystem functions in the barely vegetated and little developed soils. Besides their profound impacts on nutrient cycling, they also provide habitats and activity hotspots for unique soil microbial communities. Yet, the effects of biological soil cover on the physical and chemical soil environment and belowground microbial communities have not been comprehensively studied in this fragile ecosystem. We here address the research question how biocrusts and mosses shape the quantity and structure of the soil organic matter pool, and the activity and composition of subjacent microbial communities. Towards this end, we sampled soils under two common, but physiologically distinct moss species, Polytrichastrum alpinum and Sanionia unicinata , and adjacent biological soil crusts at two sites on Deception Island, South Shetland Islands. We found that biocrusts and mosses differentially influenced central soil properties and subjacent soil microbial communities. All major SOM compound groups (carbohydrates, aromatics and phenols, lipids, N-containing polymers) as well as microbial biomass were more abundant in soil under biocrusts. However, microbial mass-specific growth rates were higher in soil under mosses. Our results showed moss-species-specific effects in addition to effects of soil cover type, as P. alpinum affected the activity and structure of soil microbial communities and the composition of soil organic matter stronger than S. unicinata. Our study highlights the interconnectedness between soil cover and soil biogeochemistry, which is crucial for deepening our understanding of belowground functioning in Antarctic soils. This linkage is of particular importance in the context of ongoing rapid climate change on the Antarctic Peninsula, as future shifts in the distribution and abundance of soil cover may substantially impact multiple soil processes in this vulnerable ecosystem. [ABSTRACT FROM AUTHOR]