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For the food sector, onion rejects are an appealing source of value-added byproducts. Bioactive compounds were recovered from yellow onion rejects using a pulse electric field process at 6000 v and 60 pulses. The onion extract was encapsulated with whey protein isolate (WPI), pectin (P), and sodium caseinate (SC) with a mass ratio of 1:5 (extract/wall material, w/w). A Simplex lattice with augmented axial points in the mixture design was applied for the optimization of wall material for the encapsulation of onion reject extract by freeze-drying (FD). The optimal wall materials were 47.6 g/100 g (SC), 10.0 g/100 g (P), and 42.4 g/100 g (WPI), with encapsulation yield (EY) of 85.1%, total phenolic content (TPC) of 48.7 mg gallic acid equivalent/g DW, total flavonoid content (TFC) of 92.0 mg quercetin equivalent/g DW, and DPPH capacity of 76.1%, respectively. The morphological properties of the optimal encapsulate demonstrated spherical particles with a rough surface. At optimal conditions, the minimum inhibitory concentration (MIC) of the extract (mean diameter of inhibition zone: 18.8 mm) was shown as antifungal activity against Aspergillus niger. [ABSTRACT FROM AUTHOR]