Nowadays, the development of innovative food products with positive health effects is on the rise. Consequently, the aim of this study was a formulation of aggregates based on tart cherry juice and dairy protein matrix to investigate whether different amounts (2% and 6%) of protein matrix have an impact on the adsorption of polyphenols as well as on the adsorption of flavor compounds. Formulated aggregates were investigated through high-performance liquid chromatography, spectrophotometric methods, gas chromatography and Fourier transform infrared spectrometry. The obtained results revealed that with an increase in the amount of protein matrix used for the formulation of aggregates, a decrease in the adsorption of polyphenols occurred, and, consequently, the antioxidant activity of the formulated aggregates was lower. The amount of protein matrix additionally affected the adsorption of flavor compounds; thus the formulated aggregates differed in their flavor profiles in comparison with tart cherry juice. Adsorption of both phenolic and flavor compounds caused changes in the protein structure, as proven by recording IR spectra. Formulated dairy-protein-based aggregates could be used as additives which are enriched with tart cherry polyphenols and flavor compounds.