•Primary succession models focus on aboveground vascular plants. However, the prevalence of mosses and lichens, i.e. cryptogams, suggests they play a role in soil successions. Here, we explore whether effects of cryptogams on belowground microbes can facilitate progressive shifts in sand dune succession.

•We linked aboveground vegetation, belowground bacterial and fungal communities, and soil chemical properties in six successional stages in Arctic inland sand dunes: bare sand, grass, moss, lichen, ericoid heath and mountain birch forest.

•Compared to the bare sand and grass stages, microbial biomass and the proportion of fungi increased in the moss stage, and later stage microbial groups appeared despite the absence of their host plants. Microbial communities of the lichen stage resembled the communities in the vascular plant stages. Bacterial communities correlated better with soil chemical variables than with vegetation and vice versa for fungal communities. The correlation of fungi with vegetation increased with vascular vegetation.

•Distinct bacterial and fungal patterns of biomass, richness, and plant‐microbe interactions showed that the aboveground vegetation change structured the bacterial and fungal community differently. The asynchrony of aboveground vs. belowground changes suggests that cryptogams can drive succession towards vascular plant dominance through microbially mediated facilitation in eroded Arctic soil.