<p>In Okinawa Main Island, the effect of biological soil disinfestation (BSD) using ethanol solution on Jahgaru soil was elucidated. In Miyako Island, a part of Okinawa Prefecture, farming land is covered with a dark-red neutral soil, which is known as Shimajiri Mahji soil. Bitter gourd (<i>Momordica charantia</i> L.), Goya, is a popular vegetable in Okinawa and is commonly cultivated on Shimajiri Mahji soil in Miyako Island. However, several diseases, such as Fusarium wilt by <i>Fusarium cugenangense</i>, bacterial wilt by <i>Ralstonia solanacearum</i>, and root-knot disease by plant-parasitic nematodes, often occur when Goya is cultivated. Weeds around cultivated Goya often prevent its growth and reduce yield production. In this study, the detailed conditions of BSD using ethanol solution, which are suitable to Shimajiri Mahji soil in Miyako Island, were investigated to elucidate the effect of BSD against bitter gourd diseases and weed germination. Results indicated that BSD with air leakage considerably weakens its effects against diseases and that BSD with a larger air space below the cover after application (a lower volume of ethanol solution) further weakens the effects. Moreover, ethanol with a concentration ranging from 0.5% to 2.0% (not 0.25%) should be used to achieve more positive effects against <i>Fusarium cugenangense</i>, <i>Ralstonia solanacearum</i>, and plant-parasitic nematodes. In addition, BSD-treated soil irrigated with 0.5% ECOLOGA ~ L® (corresponding to 0.5% ethanol solution) in the field sterilized these pathogens and plant-parasitic nematodes and completely prevented weed germination. In particular, soaking soil thoroughly with 0.5%–2.0% EtOH is necessary to sterilize <i>Ralstonia solanacearum.</i> In conclusion, BSD using ≥ 0.5% ECOLOGA ~ L® by soaking Shimajiri Mahji soil thoroughly had significant effects on soil-borne plant pathogens of bitter gourd, plant-parasitic nematodes, and weed germination in the field in Miyako Island.</p>