Honey from the nectar of the Manuka tree (Leptospermum scoparium) grown in New Zealand contains high amounts of antibacterial methylglyoxal (MGO). MGO can react with proteins to form peptide-bound Maillard reaction products (MRPs) such as N^ϵ-carboxyethyllysine (CEL) and “methylglyoxal-derived hydroimidazolone 1” (MG-H1). To study the reactions of MGO with honey proteins during storage, three manuka honeys with varying amounts of MGO and a kanuka honey (Kunzea ericoides) spiked with various MGO concentrations up to 700 mg/kg have been stored at 37 °C for 10 weeks, and the formation of protein-bound MRPs has been analyzed via high-performance liquid chromatography-mass spectrometry (HPLC-MS/MS) following isolation of the protein fraction and enzymatic hydrolysis. During storage, contents of protein-bound CEL and MG-H1 increased continuously, directly depending on the MGO content. For honeys with large amounts of MGO, a slower formation of N^ϵ-fructosyllysine (FL) was observed, indicating competing reactions of glucose and MGO with lysine. Furthermore, the lysine modification increased with storage independently from the MGO concentration. Up to 58-61% of the observed lysine modification was explainable with the formation of CEL and FL, indicating that other reactions, most likely the formation of Heyns products from lysine and fructose, may play an important role. Our results can contribute to the authentication of manuka honey.