Conversion of dihydroxyacteone (DHA) to methylglyoxal (MGO) has been shown to be the key mechanism for the growth in "apparent" C-4 sugar content in nonperoxide activity (NPA) manuka honey. This reaction is enhanced by heating and storage time and is demonstrated for the first time in clover honey adulterated with DHA purchased from a chemical supplier and in manuka honey containing naturally occurring DHA and MGO. After heating at 37 °C for 83 days, pure clover honey with no added DHA has the same apparent C-4 sugar content as at t = 0 days. The same clover honey adulterated with synthetic DHA added at t = 0 days and heated at 37 °C over the same time scale shows a change in apparent C-4 sugars from 2.8 to 5.0%. Four NPA manuka honeys heated over longer periods show an increase in apparent C-4 sugars of up to 280% after 241 days. This study strongly suggests that a protein fractionation effect occurs in the conversion of DHA to MGO in higher NPA manuka honey, rendering the remaining δ(13)C protein value more negative and falsely indicating C-4 sugar addition when using the AOAC 998.12 method.