Moss–cyanobacteria associations serve as significant nitrogen fixers and represent the primary nitrogen sink in boreal forests. Fungi, which are essential for soil biogeochemical cycling, have community structures intrinsically linked to forest ecosystem health and productivity. Using high-throughput sequencing, we investigated differences between moss-covered and non-moss soils in two alpine forests (both plantation and natural forests) by examining soil nitrogen contents, fungal community structure, composition, and functional guilds. Results demonstrated that moss cover enhanced soil nutrient contents, including total carbon, total nitrogen, and inorganic nitrogen. It also altered fungal community characteristics, resulting in higher Chao1 and Shannon diversity indices, as well as a more complex fungal network. Notable changes in functional guilds included an increase in saprotrophic fungi abundance and a decrease in ectomycorrhizal fungi. Our findings support the concept that moss cover creates distinct soil environments: moss-covered soils attract decomposers and nutrient-mobilizing fungi (particularly saprotrophs and ectomycorrhiza), while non-moss soils favor ectomycorrhizal fungi that relieve nutrient limitation through extensional mycelial networks. These findings highlight the critical role of moss cover in sustaining forest soil health and resilience, positioning it as a cornerstone of carbon and nutrient cycling within forest ecosystems.
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