White-flesh (Hylocereus undatus; WF) and red-flesh (Hylocereus polyrhizus; RF) dragon fruit purees were subjected to heat treatment for 0 to 60 min at temperatures between 50 and 90 °C. The influence of the different heat treatments on the physicochemical properties, colour, betacyanins content, microbial destruction, antioxidative properties and rheological parameters were investigated. The physicochemical values and antioxidative properties of the unheated RF were significantly higher than that of the unheated WF (p < 0.05). The betacyanins content of RF after 90 °C for 60 min decreased to 32.35%, based on the initial puree. Total colour change (TCC) and betacyanins degradation followed the second-order kinetic. The L* and b* values of the purees can be recommended as an online quality control (R 2 ≥ 0.7733) and TCC of RF can be used to predict the betacyanins content (R 2 = 0.9442). The antioxidative properties of the heated WF and RF increased with heating treatment. The linear correlation among the antioxidative properties was strong (R 2 ≥ 0.8587). WF and RF showed shear thinning behaviour. After heating, the apparent viscosity of WF and RF increased and all cases fitted very well with the power law model (R 2 ≥ 0.9988). Thus, the heated dragon fruit purees, particularly the RF, offer possibilities to be applied in foodstuffs due to their interesting physicochemical properties and nutritional attributes after thermal treatment.