Background <p>Soybean–maize rotation is an effective strategy for addressing the challenges associated with continuous soybean cropping. However, the effects of maize frequency in cropping sequences on soil fungal functions and their associations with soybean yields remain unclear. Through a 12-year field study comparing continuous soybean (CS), maize–soybean (MS), and maize–maize–soybean (MMS) systems, fungal community functions, system-specific taxa, and bacterial–fungal inter-kingdom co-occurrence patterns were analyzed.</p> Results <p>In contrast to conventional assumptions, CS enriched symbiotic fungi and suppressed pathogens, suggesting adaptive disease resilience. Integrating maize into soybean cropping systems increased the complexity of bacterial–fungal cross-kingdom co-occurrence networks. While the MS system increased the relative&#xa0;abundances of plant pathogens and saprotrophs, the MMS system stabilized fungal functions and inhibited plant pathogen accumulation. The system-specific taxa identified in the CS and MMS systems included potential plant growth-promoting microbes and were associated with the relative&#xa0;abundances of pathogens and saprotrophic fungi as well as soybean yield. This relationship may represent a critical link between fungal function and soybean production.</p> Conclusions <p>These findings indicate that integrating maize into soybean rotations, especially in the MMS system, can stabilize fungal functions and mitigate pathogen accumulation, ultimately increasing soybean yield. These results underscore the importance of tailored crop rotation practices to optimize soil microbial communities for sustainable agricultural production.</p> Graphical Abstract <p></p>