Carboxylic acid leaching has been established eco-friendly pre-treatment method for producing biogenic silica (BSi) from rice husk. The most urgent issue is for carboxylic acid to promote new readily biodegradable acids and enhance carboxylic acid sustainability in BSi preparation. This research investigates gluconic acid (GA) applicability for biogenic silica preparation from rice husk compared with citric acid (CA). The results demonstrated that GA was preferable to CA on BSi recovery with 89.91% efficiency. Although GA leaching promoted slightly higher silica loss, the primary metal alkali impurities, such as K2O, Na2O, and Al2O3, were effectively removed at 92–93%, 89–93%, 95–97%, respectively. The combination effect of silica loss and high removal impurities resulted in lower rice husk thermal decomposition activation energy. The characteristics of BSi prepared by GA leaching were comparable with CA leaching, mainly mesoporous with 114.06 m2/g of specific surface area and 0.23 cm3/g of the pore volume. In addition, GA leaching was environmentally better than CA leaching, indicated by minor contribution to all environmental impact indices. The findings suggested that GA could be a potential replacement for prevalent carboxylic acids in BSi preparation.