Provided is a method which allows, for example, suppression of foaming in the purification step such as distillation and continuous operation, as well as direct treatment of a waste liquid (can liquid) without having to subject the same to an extra purification treatment by removing the microorganisms, nitrogen compounds, and phosphorous compounds at once from an organic substance-containing liquid obtained from microbial fermentation. Also disclosed is a method for producing an organic substance, comprising a microbial fermentation step, a separation step, a liquefaction step, and a second purification step, wherein the concentration of the nitrogen compound in the second can liquid is 0 to 150 ppm based on the total mass of the second can liquid, and the concentration of the phosphorous compound in the second can liquid is 0 to 5 ppm based on the total mass of the second can liquid.