The demand for bee products has been growing, especially regarding their application in complementary medicine. Apis mellifera bees using Baccharis dracunculifolia D.C. (Asteraceae) as substrate produce green propolis. Among the examples of bioactivity of this matrix are antioxidant, antimicrobial, and antiviral actions. This work aimed to verify the impact of the experimental conditions applied in low- and high-pressure extractions of green propolis, using sonication (60 kHz) as pretreatment to determine the antioxidant profile in the extracts. Total flavonoid content (18.82 ± 1.15–50.47 ± 0.77 mgQE·g⁻¹), total phenolic compounds (194.12 ± 3.40–439.05 ± 0.90 mgGAE·g⁻¹) and antioxidant capacity by DPPH (33.86 ± 1.99–201.29 ± 0.31 µg·mL⁻¹) of the twelve green propolis extracts were determined. By means of HPLC-DAD, it was possible to quantify nine of the fifteen compounds analyzed. The results highlighted formononetin (4.76 ± 0.16–14.80 ± 0.02 mg·g⁻¹) and p-coumaric acid (<LQ—14.33 ± 0.01 mg·g⁻¹) as majority compounds in the extracts. Based on the principal component analysis, it was possible to conclude that higher temperatures favored the release of antioxidant compounds; in contrast, they decreased the flavonoid content. Thus, the obtained results showed that samples pretreated with 50 °C associated with ultrasound displayed a better performance, which may support the elucidation of the use of these conditions.