Quinones are electrophilic compounds that can undergo Michael addition or Schiff base reaction with nucleophilic amines, but the effect of temperature has not been systematically studied. The aim of this study was to characterize how temperature affects the reaction mechanism and kinetics of 4-methylbenzoquinone (4MBQ) with lysine (Lys), Nα-acetyl Lys or Nε-acetyl Lys. The products were identified and characterized by LC-MS/MS, which revealed formation of Michael addition products, Schiff base, and a di-adduct in Lys and Nα-acetyl Lys-containing reaction mixtures. The product profiles were not affected by temperature in the range of 15–100 °C. NMR analysis proved that Michael addition of Nα-acetyl Lys occurred on the C5 position of 4MBQ. Rate constants for the reactions studied by stopped-flow UV–vis spectrophotometry under pseudo-first-order conditions where the amines were present in excess in the range 15 °C to 45 °C showed the α-amino groups of Lys are more reactive than the ε-groups. The kinetics results revealed that the temperature dependence of reaction rates followed the Arrhenius law, with activation energies in the order: Lys < Nε-acetyl Lys < Nα-acetyl Lys. Our results provide detailed knowledge about the temperature dependence of the reaction between Lys residues and quinones under conditions relevant for storage of foods.