Indonesian honey has high water content and often exceeds the limitation of standard quality appointed by national and international regulation. It is caused by the high humidity and the hygroscopic character of honey itself. Riau Province is one of the highest producers of honey, but the water content is high, about 23-27%. Heating can be used to decrease the water content, but it increases the risk of damage to honey’s secondary metabolites and may lose the functional character of honey towards human health. There is limited research that observes the effect of heating on honey’s secondary metabolites. Our research aimed to evaluate the effect of heating on Apis mellifera honey from acacia forest, Province of Riau, Indonesia towards the stability of honey’s secondary metabolites including water content analysis, screening of secondary metabolites, determination of antioxidant activity, measurement of TPC and TFC. The results show that the heating of 50 0C for 5 days and the heating of 1050C for 6 hours can decrease water content of honey without disturbing stability of honey’s secondary metabolites. It is showed by the score of IC50 of honey without heating (21103,74 μg/mL) is higher than the IC50 of honey heated by 500C (16503,83 μg/mL) and heated by 105 0C (777,33 μg/mL). The low value of IC50 indicates the high antioxidant activity, it is inline with TPC and TFC. The TPC and TFC without heating (TPC= 0,67 mgGAE/g; TFC=0,34 mgQE/g) is lower than sample heated by 500C (TPC=1,59 mgGAE/g; TFC=0,46 mgQE/g) and 1050C (TPC=13,94 mgGAE/g; TFC=4,37 mgQE/g).