In the current scenario, transforming agricultural by-products into high-value commodities is essential for preserving the environment. Plums are globally renowned for their flavor, juiciness, and nutritional value. Despite being widely popular, substantial quantities of plum kernels, rich in oils (45.95–50%) and proteins (35.9–40.0%), are underutilized due to the presence of toxic compounds like amygdalin (range 0.1–17.5 mg/g). Therefore, detoxification becomes a crucial step to mitigate the risks associated with cyanide toxicity. This study employed a response surface methodology to optimize hydrothermal treatment conditions to reduce amygdalin levels. Despite the significant reduction of 68.72 %, none of the treatment conditions reduced amygdalin to below the allowed limits. On the contrary, microwave heating at 540 W for 6 min also showed a considerable reduction of 67.90% in amygdalin but not within the permissible limits, and the prolonged heating caused burning spots on the samples. However, a combined approach involving microwave heating at 450 W for 6 minutes and hydrothermal treatment at 45 °C for 10 hours reduced the amygdalin levels to undetectable levels. These detoxified samples exhibited significant quantities of high-quality dietary proteins (32.09 %), crude fat (45.14%), crude fibre (4.16%), total ash (2.16%), carbohydrates (7.19%), and bioactive compounds, representing valuable resources for human nutrition and food industry applications. Isolated proteins from detoxified plum kernel meal displayed notable antioxidative properties alongside their nutritional and functional attributes, making them attractive ingredients for various product formulations. The purity, yield, and solubility of protein isolate from detoxified plum kernel meal at a pH of 10.5 were 90.49 %, 26.45 %, and 66.36 %, respectively. The protein isolate was rich in essential amino acids. This study underscores the potential of detoxified plum kernels as a sustainable source of essential nutrients and functional additives, contributing to advancing Sustainable Development Goals through innovative agricultural revalorization practices.