Soybean oil isolated by enzyme-assisted aqueous extraction (EAE) was subjected to molecular distillation-induced deacidification, and the effects of evaporator temperature, scraper speed, and feed flow rate on oil quality (acid value, color, peroxide value, p-anisidine value, tocopherol content, and fatty acid content) were evaluated to determine the suitable deacidification conditions. Fatty acid content was largely unaffected by evaporator temperature and scraper speed, while an increase of these parameters decreased tocopherol content as well as acid, peroxide, and p-anisidine values and resulted in Lovibond color deepening. The increase of feed flow rate had an opposite effect on the above quality indices. As a result, molecular distillation of EAE-produced soybean oil under suitable conditions (evaporator temperature = 180 °C, scraper speed = 220 rpm, feed flow rate = 4 mL/min) was found to afford a high-quality deacidified product in an environmentally friendly way.