Enzymatic degumming is a well established process in vegetable oil refinement, resulting in higher oil yield and a more stable downstream processing compared to traditional degumming methods using acid and water. During the reaction, phospholipids in the oil are hydrolyzed to free fatty acids and lyso‐phospholipids. The process is typically monitored by off‐line laboratory measurements of the free fatty acid content in the oil, and there is a demand for an automated online monitoring strategy to increase both yield and understanding of the process dynamics. This paper investigates the option of using Near‐Infrared spectroscopy (NIRS) to monitor the enzymatic degumming reaction. A new method for balancing spectral noise and keeping the chemical information in the spectra obtained from a rapid changing chemical process is suggested. The effect of a varying measurement averaging window width (0 to 300 s), preprocessing method and variable selection algorithm is evaluated, aiming to obtain the most accurate and robust calibration model for prediction of the free fatty acid content (% (w/w)). The optimal Partial Least Squares (PLS) model includes eight wavelength variables, as found by rPLS (recursive PLS) calibration, and yields an RMSECV (Root Mean Square Error of Cross Validation) of 0.05% (w/w) free fatty acid using five latent variables.