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In this study, an alternative extraction technique, ultrasound-assisted extraction, was used to extract the polyphenolic fraction from two different residues of the candelilla plant (Euphorbia antisyphilitica). These metabolites were further analyzed to evaluate their bioactivity as antioxidants. In addition, their functional groups were identified by Fourier transform infrared (FTIR) spectroscopy. The antioxidant assays showed statistically significant differences between the phenolic extracts, with citric acid residues (CAR) exhibiting a higher oxidant effect than sulfuric acid residues (SAR). The CAR from San Jerónimo (SJ) cultivar showed decreased IC50 values (179.441 ± 7.92 μL mL−1, DPPH•), and its polyphenolic fraction was able to inhibit lipid oxidation (70.31 ± 2.50%). FTIR analysis subsequently revealed the presence of functional groups related to polyphenolic compounds, such as hydroxy, carbonyl, carbon double bond, and amine groups. In addition, FTIR spectra showed slight differences in phenolic compounds, due to the strong acid treatment involved in the extraction of wax. The present study demonstrated that candelilla by-products from citric acid-wax extraction have a polyphenolic fraction with strong antioxidant activity, which may be useful in food and pharmaceutical products.