Oxidation of omega-3 fatty acids is a major limitation on its enrichment in food and beverages. An efficient and simple method to monitor lipid oxidation in complex systems is essential to limit lipid oxidation during formulation and processing. Fish oil-in-water emulsions (20% v/v) were exposed to iron or free radical initiated oxidation. Conjugated dienes (CDs) were rapidly measured using a previously developed fat extraction method. Fourier transform infrared (FTIR) spectroscopy has been used to directly record chemical changes occurring during oxidation. Variations were noticed in different spectral regions despite the presence of broad water bands near 3400 and 1640 cm-1. Partial least squares regression (PLSR) revealed correlations between CD values and full FTIR spectra (4000-600 cm-1), and different spectral regions (e.g., 1800-1500 cm-1, 1500-900 cm-1). These correlations confirm that FTIR spectroscopy is a rapid and simple method for measuring lipid oxidation in complex foods without prior fat extraction.