Purpose A method to control soybean cyst nematode (SCN) is to grow green manure which releases hatching stimulants in the absence of host plants. We hypothesized that biochar may improve the efficacy of this control strategy. Methods We evaluated the effects of two hatch-stimulating plants (Vigna radiata and Crotalaria spectabilis) in combination with rice husk biochar on the plant growth, SCN density, and soil nematode community. Plants were cultivated in biochar-amended and unamended soils for one month and then incorporated. Soils were collected periodically for chemical properties, SCN, and nematode community assessment. Results Biochar increased total biomass of V. radiata and C. spectabilis significantly. For V. radiata alone, the number of SCN juveniles (J2) increased at three weeks and then decreased, but in biochar-amended soil J2 prevailed for three to seven weeks after residue incorporation. In soil incorporated with C. spectabilis, J2 were sustained consistently in biochar-amended soil. Nine weeks after residue incorporation, real-time PCR assays revealed that V. radiata reduced the SCN density by 96% and 91%, and that C. spectabilis reduced the SCN density by 72% and 48% with and without biochar, respectively. Incorporation of green manure in biochar-amended soil increased microbial activity and abundance of omnivorous nematodes, notably Ecumenicus and Aporcelaimellus species which were negatively correlated with the SCN density. Specifically, V. radiata increased the composite and enrichment footprints of nematodes, and omnivore and structure footprints were further increased by combination with biochar. Conclusion Biochar may improve the efficacy of a green manure-based strategy to control SCN.