In this study, effect of heat treatments (liquefaction at 55 °C for 12 h and pasteurisation at 90 °C 15 sec) on total phenolic content, antioxidant activity and phenolic compounds of astragalus and sunflower-cornflower honeys was investigated. Total phenol content and antioxidant activity of honeys were assessed by Folin-Ciocalteu and ABTS methods, respectively. Phenolic profile was determined by HPLC-DAD system. Only pasteurisation process had a significant impact on sunflower-cornflower honey with regard to total phenolic content and antioxidant activity. Protocatechuic, 4-hydroxybenzoic, caffeic, p-coumaric, and ferulic acids, rutin, kaempferol were detected in astragalus honey, while 2,5-dihydroxybenzoic, chlorogenic, caffeic, p-coumaric, and ferulic acids, apigenin, rutin, kaempferol-3-glucoside, isorhamnetin-3-glucoside, quercetin, luteolin, kaempferol were detected in sunflower-cornflower honey. Pasteurisation significantly decreased caffeic acid in astragalus honey and other detected phenolics showed no significant difference after heat treatments. The impact of liquefaction process is lower than the pasteurisation process in terms of quantitatively phenolic compounds changes.