Molybdenum (Mo) deficiency is a global problem in acidic soils, limiting plant growth, development and nutrients availability. To address this, we carried out a field study with two treatments i.e. Mo applied (+Mo) and without Mo (-Mo) treatment to explore the effects of Mo application on crop growth and development, microbial diversity, and metabolites variations in maize and soybean cropping systems. Our results indicated that the nutrient availability (N, P, K) was higher under Mo supply, leading to improved biological yield and nutrient uptake efficiency in both crops. Microbial community analysis revealed that Proteobacteria and Acidobacteria were the dominant phyla in Mo treated (+Mo) soils for both maize and soybean. These both phyla accounted together 39.43%, 57.74% in -Mo and +Mo respectively in soybean rhizosphere soil, while 44.51% and 46.64% in maize rhizosphere soil which indicates more variations among the treatments in soybean soil as compared to maize soil. At lower taxonomic, the diverse responses of the genera indicated the specific bacterial community adaptations to fertilization.Candidatus Koribacter and Kaistobacter were commonly significantly higher in both crops under Mo applied circumstances in both cropping systems. These taxa, sharing similar functions, could serve as potential markers for nutrient availability and soil fertility. Metabolite profiling revealed 8 and 10 significantly differential metabolites in maize and soybean, respectively, under +Mo treatment, highlighting the critical role of Mo in metabolite variation. Overall, these findings emphasize the importance of Mo in shaping soil microbial diversity by altering metabolite composition, which in turn may enhance the nutrient availability, nutrient uptake, and plant performance.