Microencapsulation of chokeberry extracts was performed in order to improve functionality, stability, and bioavailability of extracted polyphenols. Chokeberry fruits and juice by-product (waste) extracts were spray-dried by using two carriers, maltodextrin and skimmed milk. Morphological and physicochemical characteristics of the obtained powders were analysed. simulated digestion model was used as an indicator of polyphenolics bioavailability. The moisture content varied between 3.39 and 4.61%, zeta potential had negative values (35-39 mV), maltodetrin powders were smaller (4.27-5.12 µm) compared to skimmed ones (8.50-11.01 µm). All microparticles exhibited high encapsulation efficiency of total polyphenols and anthocyanins (73-97% and 63-96%, respectively). For both extract types, maltodextrin powders released higher phenolics content compared to skimmed milk. During digestion, maltodextrin exhibited a higher protective effect on both active compounds. Taking into account the obtained results, chokeberry polyphenols stability might be improved using spray drying technique, and maltodextrin showed better properties.