The effects of the industrial processing steps (chopping-blanching-citric acid solution addition, pressing, pasteurization, depectinization, rotary vacuum filtration, bag filter and concentration) on the total and individual phenolic compounds, flavonoids, anthocyanins, and antioxidant capacity of black carrot concentrate were investigated. Then, an anthocyanin-rich black carrot concentrate (5%) was encapsulated with the emulsion method to make thermally induced whey protein-based microcapsules; the microencapsulated back carrot concentrate was used as a natural colorant in yogurt. The degradation rates of phenolics, flavonoids, anthocyanins and antioxidant capacity (1/EC50) of black carrots from raw material to concentrate were 25, 20, 19, and 33.5%, respectively, while the browning index, which is a commercial index, increased 23% between raw materials to concentrate. Bioactive compounds were moderately affected by the processing steps with the largest changes occurring early in the process. Pasteurization at 85 degrees C/2.5 min and concentration to 63.5 Bx caused a higher rate of total phenolic and flavonoid degradation compared to anthocyanins. Encapsulated concentrate in whey hydrogels showed homogenous distribution of the pink color in yogurts when added at 5, 10, 15 and 20% capsule concentrations. In whey hydrogels, 2.0 g/kg db phenolics, 1.43 g/kg db for flavonoids, 0.86 g/kg db anthocyanin was found. (C) 2016 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.