Near-infrared spectroscopy has become a common quality assessment tool for fishmeal products during the last two decades. However, to date it has not been used for active online quality monitoring during fishmeal processing. Our aim was to investigate whether NIR spectroscopy, in combination with multivariate chemometrics, could actively predict the changes in the main chemical quality parameters of pelagic fishmeal and oil during processing, with an emphasis on lipid quality changes. Results indicated that partial least square regression (PLSR) models from the NIR data effectively predicted proximate composition changes during processing (with coefficients of determination of an independent test set at RCV2 = 0.9938, RMSECV = 2.41 for water; RCV2 = 0.9773, RMSECV = 3.94 for lipids; and RCV2 = 0.9356, RMSECV = 5.58 for FFDM) and were successful in distinguishing between fatty acids according to their level of saturation (SFA (RCV2=0.9928, RMSECV=0.24), MUFA (RCV2=0.8291, RMSECV=1.49), PUFA (RCV2=0.8588, RMSECV=2.11)). This technique also allowed the prediction of phospholipids (PL RCV2=0.8617, RMSECV=0.11, and DHA (RCV2=0.8785, RMSECV=0.89) and EPA content RCV2=0.8689, RMSECV=0.62) throughout processing. NIR spectroscopy in combination with chemometrics is, thus, a powerful quality assessment tool that can be applied for active online quality monitoring and processing control during fishmeal and oil processing.