Background and aims Soil acidification is a natural process that can be accelerated by intensive nitrogen fertilization. Lime application is a typical agricultural practice to enhance soil pH and increase nutrient availability for crop production. Our study aims to reveal how liming altered soil microbial community composition and potential function in the bulk and rhizosphere soils of soybean growing in an acid black soil. Methods A short-term soybean pot experiment was conducted in an acid black soil with the amendment of five different dosages of lime. Soybean plants were harvested and soil samples were collected at the initial flowering stage. Plant biomass, shoot height and root length, as well as soil chemical properties and total microbial activities of bulk soils were measured. The abundance and composition of microbial communities in bulk and rhizosphere soils were determined using qPCR and Illumina MiSeq sequencing, respectively. Results Liming significantly increased soybean growth and soil microbial activities, and altered soil properties such as soil pH, available phosphorus (AP), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N). Lime addition increased soil bacterial abundance and decreased fungal abundance in the bulk soils, but had no effect on microbial abundance in the rhizosphere soils as well as alpha-diversity of soil microbial community. Microbial community structures in bulk and rhizosphere soils were significantly varied with lime amendment that were related to soil chemical properties, of which soil pH was detected as the most important soil factors. In addition, liming significantly increased the potential functions of amino acid, cofactors and vitamins mechanisms of bacterial communities and the guild abundance of AM fungi. Conclusions Lime application altered soil properties, increased soil microbial activities, and changed soil microbial compositions and potential functions, which eventually resulted in the improvement of soybean plant growth.