Changes in qualities of ‘Red Fuji’ and ‘Golden Delicious’ apples in response to different heat treatments (45 and 60 °C) following cold storage were investigated. Quality indices including firmness, titratable acidity, total phenolic content, antioxidant capacity, colour parameters and microstructure were measured. Results indicated heat treatment at both temperatures for 3-h hastened loss of titratable acidity in ‘Red Fuji’ and ‘Golden Delicious’ apples, but maintained firmness in both cultivars. However, heat treatment at lower temperature (45 °C) best maintained total phenolic compounds and antioxidant capacity in ‘Red Fuji’ apples throughout storage, whereas there was no difference between heat treatments in ‘Golden Delicious’ apples. Examination by scanning electron microscope (SEM) revealed that the effect of heat treatment at different temperatures on ‘Red Fuji’ and ‘Golden Delicious’ apples was structurally different. Apple tissue that had been heat treated at elevated temperature (60 °C) for 3 h was associated with fractured cell walls and collapse of cells.