Summary This study investigates how agricultural disturbance influences arbuscular mycorrhizal (AM) fungal diversity, biomass, and community niche structure. Utilizing niche concepts, we show that the AM fungal communities in intensively managed soils exhibited larger niche volumes and an increased proportion of culturable taxa, which negatively impacted biomass production. This process was primarily driven by the reduction in specialist taxa, indicating a functional homogenization of the community. Intensively disturbed low‐biomass AM fungal communities were composed of species that can persist under low host abundance. Our findings reveal that intensive management disturbance significantly decreased AM fungal species richness and biomass simultaneously. Preserving AM fungal diversity is essential for maintaining their biomass and functionality, underscoring the detrimental effects of intensive agricultural practices on these critical soil organisms and their potential consequences for soil health and ecosystem functioning.