Honey is usually subjected to filtration and heating for bottling before commercialization. However, there is no standard procedure available for thermal treatment on honey. Honey is thermally heated at various temperature and duration based on individual experience to prolong the shelf life of honey in the market. The heating methods might decrease the biochemical components such as nutrients, enzymatic activities and vitamins to certain extent. In addition to water reduction, thermal treatment on sugar rich honey usually accompanied by the formation of 5-hydroxymethylfurfural (HMF). In the present study, the biochemical components in three commonly consumed honey in Malaysia, namely tualang, gelam and acacia honey were investigated before and after thermal treatment at 90oC for 30 min. The short period of heating time was found to degrade nutrients, enzymatic activities and water soluble vitamins in honey. The degradation of protein and enzyme via proteolytic digestion had attributed to the increase of free amino acids in honey. Based on the multivariate analysis, the most thermally affected biochemical components are crude fat, panthotenic acid (Vitamin B5) and diastase activity which explain for 86.4% of the total variance. The kinetic studies on the HMF formation revealed that the honey samples followed zero order kinetic model for the first 60 min of heating at 90oC. The findings indicate that the temperature and duration of heating during honey processing is essential to be investigated according to the honey origin. The initial biochemical composition of honey would affect the kinetic profile of HMF formation.