The dataset used in this study was generated from field experiments conducted during the 2022 and 2023 cropping seasons at three locations in the Assosa area, northwestern Ethiopia. The study evaluated the effects of integrated soil fertility management practices on soybean growth, nodulation, soil properties, and yield under acidic soil conditions. Data were collected from a randomized complete block design with three replications and included treatment effects of lime, biochar, vermicompost, Rhizobium inoculation, and mineral fertilizers. Both pre-planting and post-harvest soil samples were analyzed for physical and chemical properties, while crop data included phenological traits, plant height, nodulation parameters, biomass, grain yield, and yield components. Economic variables such as input costs, grain price, and profitability indicators were also recorded for partial budget analysis. The dataset was organized and analyzed using Microsoft Excel and R software.