Conventional agricultural practices rely on the usage of synthetic herbicides to control weed proliferation in the absence of mulching, potentially leading to soil dysbiosis. Conversely, the technique of straw mulching entails the application of a substantial layer of material over the soil. The effects of different mulch types on the bacterial and fungal community distributions vary. Additionally, there is a lack of information on how agricultural straw mulching impacts the makeup of soil microbial populations. Hence, it is crucial to identify the types of mulches that enhance soil quality by influencing different microbial populations. The study investigated the effects of straw mulching, various mulching methods, and absence of mulching on the soil microbial populations within three distinct agricultural systems. Fifteen soil samples were procured from gardens situated in Iowa, USA. For every individual specimen, soil specimens were procured from six distinct locations and amalgamated. DNA was extracted and analyzed the taxonomic assessment of both bacterial and fungal. Straw mulching showed considerably greater levels of Actinobacteria (p < 0.000001), Proteobacteria (p < 0.0001), Ascomycota (p < 0.000001), and Basidiomycota (p < 0.01) when compared with other mulching. The most elevated bacterial and fungal diversity were discovered in straw mulching, as evidenced by the elevated values of the Chao1 and Shannon indices (p < 0.001). Linear discriminant analysis showed significantly higher levels of beneficial microbes including nitrogen-fixing bacteria (p < 0.008) in straw mulching. To summarize, our results indicated that agricultural straw mulching induced alterations in bacterial composition and enhancements in fungal presence compared to the microbiota of other mulching methods and no mulching.