Fish- or algal oils have become a common component of infant formula products for their high docosahexaenoic acid (DHA) content. DHA is widely recognized to contribute to the normal development of the infant, and the European Commission recently regulated the DHA content in infant formulas. For many manufacturers of first-age early life nutrition products, a higher inclusion level of DHA poses various challenges. Long-chain polyunsaturated fatty acids (LC-PUFAs) such as DHA are very prone to oxidation, which can alter the organoleptic property and nutritional value of the final product. Traditional methods for the assessment of oxidation in complex systems require solvent extraction of the included fat, which can involve harmful reagents and may alter the oxidation status of the system. A rapid, efficient, non-toxic real-time method to monitor lipid oxidation in complex systems such as infant formula emulsions would be desirable. In this study, infrared spectroscopy was therefore chosen to monitor iron-induced oxidation in liquid infant formula, with conjugated dienes and headspace volatiles measured with GC-MS as reference methods. Infrared spectra of infant formula were recorded directly in mid- and near-infrared regions using attenuated total reflectance Fourier-transform (ATR-FTIR) and near-infrared (NIRS) spectrophotometers. Overall, good correlation coefficients (R2 > 0.9) were acquired between volatiles content and infrared spectroscopy. Despite the complex composition of infant formula containing proteins and sugars, infrared spectroscopy was still able to detect spectral changes unique to lipid oxidation. By comparison, near-infrared spectroscopy (NIRS) presented better results than ATR-FTIR: prediction error ATR-FTIR 18% > prediction error NIRS 9%. Consequently, NIRS demonstrates great potential to be adopted as an in-line or on-line, non-destructive, and sustainable method for dairy and especially infant formula manufacturers.