Plant-based proteins are gaining in attraction compared with animal-based proteins due to their superior ethical profiles, growing concerns on the part of various organizations about animal health and welfare, and increased global greenhouse-gas emissions in meat production. In this study, the response surface methodology (RSM) using a Box–Behnken design (BBD) was applied to optimize the ultrasound-assisted alkaline extraction of cherimoya-seed proteins as valuable by-products. The effects of three pH, temperature, and time factors on the protein-extraction yield and protein content were investigated. The pH at 10.5 and temperature of 41.8 °C for 26.1 min were considered the optimal ultrasound-assisted alkaline-extraction conditions since they provided the maximum extraction yield (17.3%) and protein content (65.6%). An established extraction technique was employed to enhance the cherimoya-seed protein yield, purity, and functional properties. A thermogravimetric analysis (TGA) of the samples showed that the ultrasound-assisted alkaline extraction improved the thermal stability of the protein concentrate.