Currently, the utilization of agro-industrial by-products has gained popularity due to the presence of bioactive compounds such as polyphenols. In this context, processing residues from green kiwi (Actinidia deliciosa) and yellow kiwi (Actinidia chinensis), including peels and bagasse, represent an underutilized source of bioactive compounds, especially flavonoids with proven antioxidant and anti-inflammatory properties. To obtain these compounds, the optimization of the parameters involved in the extraction process, such as temperature, time, and solvent concentration, plays a crucial role in identifying the best conditions and potential interactions to maximize the desired results. This is key to the circular economy and food innovation. The main objective of this work was to optimize the recovery of flavonoids using the heat-assisted extraction (HAE) technique, considering time (5–60 min), temperature (30–90 ºC), and solvent concentration (0–100% ethanol) as variables to be optimized, in four kiwifruit by-products—green kiwifruit peel (GKP), green kiwifruit bagasse (GKB), yellow kiwifruit peel (YKP) and yellow kiwifruit bagasse (YKB)—using Response Surface Methodology (RSM). HPLC-ESI-QqQ-MS/MS was used to identify and quantify three main flavonoids: epigallocatechin, rhoifolin, and dihydroisorhamnetin. The data show that YKP concentrates the highest amount of total flavonoids (33.2 µg/ml of extract) among the matrices evaluated, with epigallocatechin being the main flavonoid, reaching a concentration of 16.01 µg/ml of extract, being of importance since this compound has high antioxidant capacity and is associated with cardioprotective, anti-inflammatory, and neuroprotective effects. The experimental conditions that allowed the highest recovery of flavonoids were 5 minutes, 30 °C, and 100% ethanol as solvent. These results represent an opportunity to enhance the value of yellow kiwifruit peel by incorporating it into functional food, nutraceuticals, and even cosmetic formulations, aligning with trends in sustainability, waste reduction, and the development of high-value bioactive ingredients with a positive impact on health and sustainability.