Biochar effects on legume growth and biological nitrogen fixation have been studied extensively, mostly in acidic soils with laboratory produced biochar. In the present study, a pot experiment in a full factorial experimental design was performed to examine soybean yield and nodulation of three genotypes grown with or without biochar and NPK fertilizers in an alkaline soil. We observed synergistic effects of biochar and NPK fertilizer applications on biomass and seed yields for all three soybean genotypes. Total biomass production and seed yield increased on average by 67% and 54%, respectively, with biochar and by 201% and 182% with NPK fertilizer application compared to the control. When applications of biochar and NPK fertilizer were combined, the increases were 391% and 367%, respectively. However, the biomass production in the control was very low (692 kg ha−1) due to a high soil pH (8.80). The nodulation increased with biochar and NPK fertilizer applications, and was largest with the combined application. A correlation was found between leaf chlorophyll content (single photon avalanche diode value) and nodule number. We suggested that the synergistic increase in yield was due to a decrease in soil pH caused by biochar and NPK fertilizer applications thereby increasing P availability in this alkaline soil.