Formation of Maillard reaction products (MRPs) is increasingly studied by the use of fluorescence spectroscopy, and most often, by measuring single excitation/emission pairs or use of unresolved spectra. However, due to the matrix complexity and potential co-formation of fluorescent oxidation products on tryptophan and tyrosine residues, this practice will often introduce errors in both identification and quantification. The present study investigates the combination of fluorescence excitation emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC) to resolve the EEMs into its underlying fluorescent signals, allowing for better identification and quantification of MRPs. EEMs were recorded on a sample system of bovine serum albumin incubated at 40 °C for up to one week with either glucose, methylglyoxal or glyoxal added. Ten unique PARAFAC components were resolved, and assignment was attempted based on similarity with fluorescence of pure standards of MRPs and oxidation products and reported data from literature. Of the ten fluorescent PARAFAC components, tyrosine and buried and exposed tryptophan were resolved and identified, as well as the formation of specific MRPs (argpyrimidine and Nα-acetyl-Nδ-(5-methyl-4-imidazolon-2-yl)ornithine) and tryptophan oxidation products (kynurenine and dioxindolylalanine). The formation of the PARAFAC resolved protein modifications were qualitatively validated by liquid chromatography-mass spectrometry.