A significant increase in interest in food-derived peptides obtained mostly through enzymatic reactions has been observed in the past few years. One of the best sources of bioactive peptides are defatted egg yolk proteins, which can potentially find application as high-quality nutritional supplements for infants with cow’s milk protein intolerance and as natural preservatives. The aim of this study was to obtain peptides from defatted egg yolk protein, to study their antioxidant and antimicrobial properties, and to identify peptides with bioactive properties To control the course of the process, MALDI-TOF/MS (matrix-assisted laser desorption/ionization time-of flight/mass spectrometry) spectra were also examined. The peptide mixture obtained through enzyme digestion was tested for its antioxidant properties by measuring the scavenging activity in 2,2-diphenyl-1-picrylhydrazyl radical (DPPH•), 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) radical cation decolorization (ABTS•+), and ferric reducing activity (FRAP) assays. Antimicrobial activity was also studied. The peptide mixture exhibited significant antioxidant activity: DPPH—1776.66 ± 32.99, ABTS—390.43 ± 8.92, and FRAP—16.45 ± 0.19. The inhibition of bacterial growth by two concentrations of the peptide mixture was examined. The best result was obtained in Bacillus cereus, with an inhibition zone of 20.0 ± 1.0 and 10.7 ± 0.6 mm at the concentrations of 50 and 25 mg/mL, respectively. The results of the study suggest that the mixture of egg yolk peptides may exhibit a number of health-promoting properties