The importance of bioactive compounds such as betalains and anthocyanins was highlighted in the present study by the valorization of red beetroot and sour cherry as an attempt to develop healthy products. The aim of the study was to obtain and characterize three types of marmalade based on red beetroot, sour cherry and both in 1:1 combination, obtained by heating at 95 °C for 30 min. Changes in total phenolic content, total flavonoids, betalains, anthocyanins and antioxidant activity were evaluated before and after the thermal treatment. Several other analyses such as color, rheological and textural analyses and confocal laser microscopy were performed to provide further information about the quality of the added-value food products. A significant decrease of 34% in betalains content was registered in the red beetroot marmalade due to the chemical changes in bioactives induced by the temperature. A satisfactory ABTS radical scavenging activity of 8.12 ± 0.38 mMol Trolox/g dry weight (dw) was obtained for the red beetroot and sour cherry based marmalade. The gelled structure was validated by the rheological and textural characteristics. The results highlighted the potential use of red beetroot and sour cherry as food raw materials, due to their particular profile of bioactive compounds.