A comprehensive study regarding the microencapsulation of bioactives from elderberry extract (Sambuci nigra) by whey proteins was performed. Quenching experiments allowing the estimations of binding parameters for anthocyanins and flavonoids from elderberry extract by whey proteins isolate were first performed. The binding parameters values highlighted a preferential binding of the flavonoids, whereas a dynamic quenching process involving multiple binding sites was suggested. The HPLC analysis allowed identification of major anthocyanins and flavonoids in the extract, as delphinidin-3-glucoside and catechin hydrate. Molecular docking tests carried out to identify the particularities of the interaction between these bioactives from elderberry by beta-lactoglobulin indicated affinity varying with the type of complex and different binding sites for each ligand. The results indicated that the complex with anthocyanins is thermodynamically stable, while the complex with the main flavonoid appears rather unstable. Further, elderberry bioactives were encapsulated within whey proteins isolate and pectin, with an encapsulating efficiency of similar to 98%. The confocal laser scanning microscopy revealed the presence of various spherical or polygonal formations with sizes ranging from 40 to 150 mu m. The powder showed a significant amount of polyphenols (5.59 +/- 0.02 mg GA/g DW), flavonoids (1.19 +/- 0.02 mg CE/g DW) and anthocyanins (307.82 +/- 1.57 mg OG/g DW), whereas the antioxidant activity was 3695.67 +/- 0.67 mu M Trolox/g DW. The remarkable antioxidant activity of the powder highlights the potential use of the microcapsules as natural antioxidants in food and derivatives. The thermal stability experiments evidenced a significant protective effect on anthocyanins degradation, whereas an increase in flavonoid content was found.