To assess the impacts of biochar application on crop productivity and global warming mitigation, a 4-yr field experiment was conducted in a well-drained Andosol in northern Japan. Wood residue–derived biochar (pyrolyzed at >800°C) was applied at rates of 0, 10, 20, and 40 Mg ha−1 for potatoes, winter wheat, sugar beet, and soybeans cultivated in rotation, and CO2, N2O, and CH4 emissions from the soil and yield and quality of the harvested materials were measured. Biochar application, regardless of rate, had no significant impact on yield and quality of the harvested materials, except for soybean grain yield. It also had no effect on cumulative CO2, N2O, and CH4 emissions from the soil. Andosols are inherently highly porous, and biochar application increased soil porosity only at the highest amendment level. The small changes in soil properties and the recalcitrance of the biochar’s C components probably account for the unchanged soil-associated greenhouse gas emissions and the minimal impact on crop yield and quality. Because soil CO2 emission was not increased, the net ecosystem C budget during the study period increased with the rate of biochar application from −3.55 ± 0.19 Mg C ha−1 without biochar application to 4.89 ± 0.46, 13.4 ± 0.3, and 29.9 ± 0.4 Mg C ha−1 at application rates of 10, 20, and 40 Mg ha−1, respectively; therefore, application of wood residue–derived biochar to an Andosol has great potential for mitigating global warming through enhanced soil C sequestration without sacrificing crop productivity.