Blueberry fruits are frequently processed to different products, which are subjected to different temperature regimes during their manufacture. Therefore, the aim of this study was to evaluate the impact of different temperatures (4 °C, room temperature, 50 °C, 75 °C and 100 °C) on the stability of soluble solids, pH value, color and primary and secondary metabolites in blueberry purees of three different highbush cultivars ('Bluecrop', 'Jersey' and 'Earliblue'). Soluble solids content increased with heating; conversely, 8–16% lower levels of total sugars and organic acids have been measured in purees subjected to highest temperature regimes. Blueberry purees prepared at higher temperatures were also characterized by a 11–32% decrease in total phenolic content and a lower content of all analyzed phenolic groups. A major, 38–64% decrease in total anthocyanins has been linked to darker color of purees, subjected to higher temperature. The loss of secondary metabolites was cultivar specific and higher temperatures caused a greater decrease on 'Earliblue' and 'Jersey' purees compared to 'Bluecrop' puree.