INTRODUCTION: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.OBJECTIVES: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.METHODS: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.RESULTS: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.CONCLUSION: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.