The growing demand for food and biofuels urges the vegetable oil processing industry to adopt cleaner technologies to mitigate the environmental pollution caused by chemical refining processes. Over the past decade, several enzymatic methods have proven to be efficient at reducing the generated waste, but improving the benefit-cost ratio is still necessary for the widespread adoption of this technology. In this work, we show that lecithin:cholesterol acyltransferase from Aeromonas enteropelogenes (LCAT) provides a higher extra-yield of soybean oil than a type A1 phospholipase (PLA) enzyme currently commercialized for soybean oil deep degumming. Our model indicates that crude soybean oil treated with the new enzyme generates 87% more neutral oil from phospholipids than the widely used PLA, with the corresponding reduction in waste and byproducts generation. The refined oil retains the phytosterols naturally present in crude oil, enriching its nutritional value. The results presented here position LCAT as a promising candidate to provide the green solutions needed by the industrial oil processing sector. Key points • Selected LCAT gene candidates were expressed in E. coli. • Aeromonas enteropelogenes LCAT hydrolyzes all the phospholipids present in crude soybean oil. • The LCAT enzyme provides a higher yield of neutral oil than commercial PLA enzymes and generates less waste. • The degummed oil retains sterols with high nutritional value.