© 2022 Institution of Chemical EngineersIn the present study, natural deep eutectic solvent-based ultrasound-assisted extraction was introduced for the extraction of cyanidin-3-O-glycoside from black carrots. Response surface methodology (RSM) with central composite design with 27 experimental runs were used for the optimization studies. The analysis of variance indicated that the solid/solvent ratio and ultrasound power had a significant effect on the responses. The measured parameters corresponded to the predicted results. Cytotoxicity analyzes were performed after the verification of the data obtained as a result of the optimization. Based on the results of cytotoxicity analysis, the inhibitory effect of the extracts was proven on Caco-2 and HUH7 cell lines. Microencapsulation was achieved with the complex coacervation with three different wall materials to provide ease of use and to extend the shelf life. The pH, temperature and storage stability analysis results of the samples showed that +4 °C was the best storage temperature and the total monomeric anthocyanin content of the samples decreased with increasing storage time. Based on the findings, an eco-friendly, high efficient and green metholodology alternative was offered to extract anthocyanin from food matrices.