This study optimized the extraction conditions to maximize the recovery yields of quercetin and total flavonoids from red onion skin waste using sequential microwave/ultrasound-assisted extraction. Five effective factors of quercetin extraction yield were investigated using response surface methodology. The method was successfully performed under optimal 60 s microwave irradiation conditions followed by 15 min sonication at 70 °C with 70% (v/v, water) ethanol with a solvent-to-solid ratio of 30 mL/g. The variance analysis of the model for both quercetin (Y₁) and total flavonoid (Y₂) recovery from DOS demonstrated that ultrasound temperature (X₂) was the most highly significant and influential factor, with a p-value of <0.0001 for both responses. Additionally, three key interaction terms—X₁X₂, X₂X₄, and X₂X₅—were identified as highly significant, further underscoring the critical role of ultrasound temperature in optimizing the extraction process for both quercetin and total flavonoids. The maximum recovery yields of quercetin and total flavonoids from red onion skin were 10.32% and 12.52%, respectively. The predicted values for quercetin (10.05%) and total flavonoids (12.72%) were very close to the experimental results. The recovery yields obtained from different extraction methods under the identical experimental conditions mentioned earlier were ultrasound/microwave-assisted extraction (7.66% quercetin and 10.18% total flavonoids), ultrasound-assisted extraction (5.36% quercetin and 8.34% total flavonoids), and microwave-assisted extraction (5.03% quercetin and 7.91% total flavonoids). The ANOVA confirmed highly significant regression models (p-values < 0.0001), with an insignificant lack of fit (p = 0.0515 for quercetin, p = 0.1276 for total flavonoids), demonstrating the robustness and reliability of the optimization. This study provides valuable insights for improving the extraction of bioactive compounds, which is critical for developing effective cancer treatments and advancing medical research. Additionally, the model shows potential for scaling up food processing applications to recover valuable products from red onion skin waste.