Rhizosphere microorganisms are critical for crop nutrient cycling and soil ecological functions in agroecosystem soils; however, there is limited information regarding the role of root exudates in determining soil microbial communities and functions in plant–soil systems, especially for microbial nutrient limitations. In the present study, rhizosphere soil samples were collected from the main food crop families, including maize, soybean, potato, and buckwheat, representing the cereals, Leguminosae, Solanaceae, and Polygonaceae families, in the northern Loess Plateau, China, to investigate soil microbial co–occurrences and assembly processes and the relationship between soil microbes and root exudates. The results showed that the crop families greatly regulated the soil microbial community composition and assembly, and all microorganisms of the four species were subjected to N limitation via the vector analysis. The topological properties of the soil microbial networks varied with the crop family, demonstrating that the ecological relationships of bacterial taxa are more complex than those of fungi. Stochastic processes were more important in stimulating assembly across the four crop families; the non–dominated process governed >60 % of the critical ecological turnover in community assembly, whereas dispersal limitation was the key factor influencing fungal community assembly. Furthermore, the metabolic profiles of root exudates in response to microbial N limitation varied by family. Microbial function and metabolic limitations were strongly associated with variations in root exudates, especially amino acids and organic acids, which were directly facilitated by crop families. Our results highlight the key roles of root exudates in stimulating microbial community structure and ecological functions from the perspective of microbial nutrient limitation and improve our understanding of plant–microbe interactions in agricultural ecosystems.