The Neutralization process is generally advised for neutralizing pre-to cottonseed oil to remove majority of the degummed oils or gossypol. This oil should be neutralized regularly, and have a low phosphatide content. The three free fatty acid stages are saponified with caustic soda, and sodium, depending on the subsequent bleaching method, at which point the soap is separated and neutralized along with washed oil and is then vacuum dried.

The oil is initially heated on the optimum process heater. To successfully condition the non-hydrate phosphatide, a smaller quantity of concentrated phosphoric acid is usually added and thoroughly blended with the oil. After a brief reaction period, dilute caustic soda is added to neutralize the free fatty and phosphoric acid. All oils are then processed through a separator and then into another reaction tank. The latter is recommended for oils with a correspondingly high phosphatide content. Self-cleaning separators are generally used for separating the sodium soap. However, the remaining soap content from the neutral oil is still too high for the subsequent process phases, and it must therefore be refined through 1 or 2 additional washings. To ensure the efficiency of this procedure, hot water is added and mixed with the oil. The soapy clean water is then removed an additional separator.

Typically, one scrub stage will suffice. A second wash cycle is common if small residual soap contents are needed. However, a low residual cleansing soap content can be achieved by acidifying this wash water with a citric or phosphoric acid solution. A second caustic treatment with the neutral oils is primarily applied with Crude oil, Steam Trouble or Lye.