Background: Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season. Results: The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted. Conclusions: We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.