Industrial treatments of commercial honeys during extraction and storage affect the quality of honey. One of the most common treatments in the honey industry is thermal treatment which could make some changes in the physicochemical and antioxidant properties of honey. This study was conducted to determine the effect of thermal treatment at 63 °C for 10, 20 and 30 min on physicochemical and antioxidant properties of lotus, thyme, and multifloral honeys. Samples were analyzed for pH, free acidity, moisture, hydroxymethylfurfural (HMF), color, total phenolic content, DPPH° radical-scavenging activity and ferric reducing antioxidant power (FRAP). Changes were more or less observed in all the physicochemical characteristics of honeys during the thermal treatment. However, among the physicochemical characteristics, increase in HMF content and decrease in total phenolic contents were more evident. Considering the antioxidant capacity of honeys, decreases in DPPH° radical scavenging activity of thyme honeys and FRAP values of thyme and lotus honeys during the thermal treatment were observed. Changes made in physicochemical characteristics of honeys during the thermal treatment are merely important from the standpoint of compliance with national and international legal limits. However, from the nutritional point of view, decrease in the antioxidant capacity of honeys is of particular importance and may affect the nutritional and health benefits of honey.