In this study, whey proteins hydrolysates, pectin and maltodextrin were utilized to encapsulate flavonoids extracted from yellow onions skins by freeze drying. In a first step, the phytochemicals profile, antioxidant activity of the extract and microencapsulated flavonoids were characterized. Further, the bioinformatics tools showed that the main whey proteins are highly susceptible to proteinase K hydrolysis. Three four-residues long peptides resulted through beta-lactoglobulin hydrolysis matched longer sequences indexed in PepBank, for exerting antimicrobial and angiotensin-converting enzyme inhibitory activities. Our results indicated that maltodextrin/pectin/whey proteins hydrolysates ratio of 2:1:0.4 was more efficient in encapsulation of flavonoids, with encapsulation efficiency of 66.46 +/- 0.18%. The confocal laser scanning microscopy highlighted the presence of spherical, filamentous or polygonal particles. The supplementation of fermentation medium with 0.5% of powder had a positive effect on preservation of the viability of Lactobacillus bifermentans. The stability of flavonoids during storage showed a slightly release of flavonoids in selected variants.