Abstract The application of biochar to agricultural ecosystems is a potential solution to mitigate climate change and guarantee food security. However, the impacts of biochar on greenhouse gas emissions and crop yield are usually evaluated separately and the results are contradictory in individual studies. In this study, a meta-analysis was conducted based on data from 28 peer-reviewed studies to quantify the impacts of biochar application on greenhouse gas emissions and crop yield using yield-scaled greenhouse gas intensity (GHGI). Potential factors (experimental conditions and properties of soil and biochar) influencing the effect of biochar on yield-scaled GHGI were explored. The results showed that overall, biochar significantly reduced yield-scaled GHGI by 29%. The reductions in yield-scaled GHGI induced by biochar varied with different experimental conditions and properties of soil and biochar. However, the difference was only significant between the two cropping systems, with significantly greater reduction being observed in dry lands (−41%) than in paddy fields (−17%). Therefore, it is suggested that biochar amendment in dry lands may bring more environmental and agronomic benefits than that in paddy fields. The response of crop yield to biochar application further implied that biochar made from crop residue, biochar produced at low pyrolysis temperatures (≤400 °C), and biochar with high pH (>9.0) might contribute to save the production cost of biochar while promoting crop yield in agricultural ecosystems. Long-term field trials are required to elucidate the persistence of the impact of biochar on reducing yield-scaled GHGI and to clarify the underlying mechanisms. The balance between the price of biochar production and the benefits brought by biochar should also be focused in further studies. Graphical abstract Unlabelled Image Highlights • Overall, biochar significantly reduced GHGI by 29%. • The effect of biochar on reducing GHGI was significantly affected by cropping system. • Biochar had no effect on GHGI when no nitrogen fertilizer was applied. • Properties of soil and biochar have little impact on the response of GHGI to biochar. [ABSTRACT FROM AUTHOR]