Although soil structure is essential for land sustainability, resilience, and fertility, the biological factors of aggregate formation and dynamics, especially the role of mycorrhizal fungi, are still unclear. Soils from a secondary succession, grasslands → shrublands → secondary forests → primary forests in subalpine regions, were sampled to compare the contribution of mycorrhizal fungal communities to the aggregate structure. Four aggregate size classes (>2000 and 250–2000 µm, large and small macroaggregates, respectively; 53–250 µm microaggregates; and < 53 µm silt and clay fraction) were related to microbial community structure, root biomass, and morphology, mycorrhizal infection rate, and external mycorrhizal hyphae. The proportion of large macroaggregates increased by 10 %, while small macroaggregates decreased by 9 % during vegetation succession, increasing the mean weight diameter by 17 %. The Shannon–Wiener and Chaos indexes of arbuscular mycorrhizal fungi (AMF) in grassland soil were three times and in shrubland, they were 24 times higher than in the primary spruce forests. The Simpson index of AMF had a positive linear relationship with soil structure. The mycorrhizal hyphal density was maximal in primary forests and could explain the aggregate size distribution before the arboreous layer developed. In contrast, dissolved organic carbon (DOC) and the diameter of the mycorrhizal hyphal contributed to the distribution of aggregates during later succession stages. Thus, biological aggregation mechanisms in the studied subalpine region followed ecosystem succession, with the mycorrhizal fungal communities being the crucial factor affecting the soil structure mainly during grassland and shrubland succession (AMF stage). In contrast, during the ECM stage, the contribution of DOC to aggregate formation became more critical. © 2022 Elsevier B.V.