Using natural plant extracts as food additives is a promising approach for improving food products' quality, nutritional value, and safety, offering advantages for both consumers and the environment. Therefore, the main goal of this study was to develop a sustainable method for extracting polyphenols and carotenoids from horned melon peel using the cloud point extraction (CPE) technique, intending to utilize it as a natural food additive. CPE is novel promising extraction method for separation and pre-concentration of different compounds while being simple, inexpensive, and low-toxic. Three parameters within the CPE approach, i.e., pH, equilibrium temperature, and equilibrium time, were investigated as independent variables through the implementation of Box-Behnken design and statistical analyses. The optimized conditions for the maximum recovery of both polyphenols and carotenoids, reaching 236.14 mg GAE/100 g and 13.80 mg β carotene/100 g, respectively, were a pH value of 7.32, an equilibrium temperature of 55 °C, and an equilibrium time of 43.03 min. The obtained bioactives' recovery values under the optimized conditions corresponded to the predicted ones, indicating the suitability of the employed RSM model. These results highlight the effectiveness of CPE in extracting bioactive compounds with varying polarities from agricultural by-products, underscoring its potential for enhancing the value of food waste and advancing sustainable practices in food processing. According to microbiological food safety parameters, the optimal CPE extract is suitable for food applications, while its storage under refrigerated and dark conditions is particularly beneficial. The CPE extract's enhanced stability under these conditions makes it a more viable option for long-term storage, preserving both safety and quality.