Long‐Term Management Shapes Soil Microbial Communities Primarily Through Modulating Soil Habitat Quality in Swiss Croplands

ABSTRACT Soil microbial communities are key drivers of soil functioning in agricultural systems. Yet the relative influence of soil properties and cropping practices on their diversity remains insufficiently understood. We investigated 60 cropland sites in western Switzerland, covering a broad range of soil properties and cropping practices, to explore their relationship with soil microbial communities. Rather than classifying fields into broad management systems, we adopted a multifactorial approach, considering both soil properties (SOC, texture, pH, SOC:clay ratio) and cropping practices averaged over ten years (tillage intensity, fertilization type and quantity, rotation and cover crop diversity, soil cover, temporary meadow). Our results indicate that soil properties are the primary factor influencing microbial habitat, carrying the majority of the explained variance in microbial biomass, activity, and community composition. SOC was positively correlated with microbial biomass and activity. Soil pH also positively correlated with increased microbial activity and was a key factor in shaping prokaryotic community composition. The SOC:clay ratio was significantly associated with fungal community composition. SOC and pH are shaped by long‐term agricultural practices. In contrast, the ten‐year agricultural history exhibited weaker direct associations with microbial metrics, even though it modulates microbial habitats. Temporary meadow in the rotation was most consistently linked to changes in soil microbial communities, likely reflecting broader differences in cropping system intensity. Taxa with similar ecological functions (e.g., plant‐beneficial bacteria, symbiotrophic fungi) showed a substantial heterogeneity in their response to soil and agronomic determinants, highlighting the need to investigate functional traits to better understand the link between cropping practices, microbial habitat quality, and agroecosystem functioning. Taken together, our findings underscore the need to consider soil habitat quality as the main lever to sustain microbial communities in croplands, jointly shaped by inherent soil properties and the long‐term influence of cropping practices. Future research should target microbial functional traits and field‐scale habitat characterization to help identify effective levers supporting crop productivity while maintaining sustainable agroecosystems.