Blackthorn fruits are rich source of polyphenols that exert numerous biological activities. But, diverse structure and polarity of phenolic compounds limit their extractability and bioavailability. Therefore, the efficiency of a green co-solvent β-cyclodextrin was examined in boosting the blackthorn polyphenols extraction. Compared to water, as the greenest solvent, β-cyclodextrin was the most efficient in the extraction of flavonoid glycosides quercetin 3-O-glucoside and cyanidin 3-O-glucoside with the extraction rate increase of over 50 % and 40 %, respectively. The second advantage of the β-cyclodextrin use was its intrinsic capability of si- multaneous encapsulation of the compounds, through inclusion complexes formation. Scanning electron microscopy, thermogravimetric analysis, and controlled release of the dominant blackthorn polyphenols were used for the encapsulation confirmation and physico-chemical characterization. Encapsulation process reached the efficiency of 76.73 %, providing amorphous particles in the micrometer scale. The effect of the encapsulates on the growth of human MCF7, HT-29, and MRC-5 cells was evaluated in vitro. In silico molecular docking analysis was performed to generate data about the most probable li- gand poses and binding mechanisms of β-cyclodextrin encapsulated blackthorn poly- phenols. Flavonoid glycosides were most preferably extracted and encapsulated. Rings A and C of flavonoid core enter the hydrophobic hole of β-cyclodextrin and hydrogen bonds are the most responsible for the complex stabilization.