The dataset.csv file compiles data from 26 meta-analyses that examine the effects of agroforestry on soil-related metrics at a global scale. These effects are reported both qualitatively and quantitatively, using natural log ratios accompanied by corresponding measures of uncertainty. Additionally, the dataset includes a quality assessment of each meta-analysis, based on 16 predefined criteria. It also provides a classification of effect sizes across seven soil outcome categories, various agroforestry systems, and distinct climatic regions. The primaryStudies.csv file compile the list of the primary studies provided by 22 of the 26 meta-analysis reporting on agroforestry and soil outcome that we identified. The dataset was updated to correct errors in the meta-analysis DOIs and to revise the study quality assessment ratings.