The paper presents the results of microwave irradiation and conventional heating of honey. These two kinds of thermal treatment result in the formation of 5-hydroxymethyl-2-furfural (HMF), and changes in the antioxidant potential of honeys, which were studied as well. Four types of honey (honeydew, lime, acacia, buckwheat) were analyzed. Honey samples were subjected to conventional heating in a water bath (WB) at 90 °C up to 60 min or to the action of a microwave field (MW) with constant power of 1.26 W/g of the sample up to 6 min. Changes in the antioxidant capacity of honeys were measured as a percentage of free radical (ABTS+and DPPH) scavenging ability. Changes in the total polyphenols content (TPC) (equivalents of gallic acid mg/100 g of honey) were also determined. Formation of HMF in honey treated with a microwave field was faster in comparison with the conventional process. Changes in the antioxidant properties of honey subjected to thermal or microwave processing might have been botanical origin dependent.