In this work, we studied the impact of encapsulated elderberry extracts as natural meat extenders to preserve both the quality and the oxidative stability of beef burgers. In particular, the comprehensive chemical changes of beef burgers treated with different antioxidants, namely, (a) a control without antioxidants, (b) 0.5 g/kg sodium erythorbate (ERY), (c) 2.5 g/kg encapsulated elderberry extract (EE 2.5), and (d) 5 g/kg encapsulated elderberry extract (EE 5), each one packaged under modified atmosphere (80% O2 and 20% CO2) for 13 days storage at 2 ± 1 °C, were deeply evaluated. Overall, EEs showed a wide array of antioxidant compounds, namely polyphenols like anthocyanins, flavonols, and phenolic acids. Multivariate statistics provided marked chemical differences between burgers manufactured with EEs and synthetic antioxidants (ERY) during 13-days storage in terms of both metabolomic profiles and typical lipid/protein oxidation markers (such as malondialdehyde and total carbonyls). Most of the differences could be attributed to some discriminant compounds, namely glutathione, 4-hydroxy-2-nonenal, hydroxy/peroxy-derivatives of fatty acids, carbonyl compounds (such as 5-nonen-2-one and 1,5-octadien-3-one), and cholesterol. Interestingly, significant correlations (p < 0.01) were observed between malondialdehyde, total carbonyls, and these discriminant metabolites. The combination of spectrophotometric approaches and a high-throughput untargeted metabolomics analysis outlined a strong modulation of both lipid and protein oxidations, likely promoted by the encapsulated meat extender (elderberry), thus confirming its ability to delay oxidative phenomena during the shelf-life of beef burgers.