The Maillard reaction (MR), despite its impact on flavor, color, and texture of cereal products, must be controlled for possible deleterious effects on protein nutritional quality. The present study aims to simultaneously monitor three indicators of the MR reaction (acid-released lysine, furosine, and carboxymethyllysine (CML)) by GC/MS in model cookies and evaluate the effect of formulation and baking temperature. Whereas furosine followed a bell-shape kinetic, indicative of an intermediary compound, CML linearly accumulated, proving to be a good indicator of the advanced MR. Acid-released lysine continuously decreased during baking. A reference baking level was defined to compare differently processed cookies using fluorescence synchronous spectra, highly sensitive to the dough physicochemical properties. Furosine was maximal in glucose-containing cookies, but only accounted for 5-50% lysine blockage, depending on the sugar and baking temperature. High oven temperatures and the use of fructose as the sugar source were associated with lowest the lysine damage and CML formation.