BACKGROUNDSour cherry (Prunus cerasus L.) stones are the major byproduct of the cherry industry and the efficient management of this biowaste can lead to achieving the food processing sustainability aimed at by the modern food industry. Despite its significant content of lipids, the valorization of cherry stone waste as feedstock for lipid extraction appears to be limited due to the high moisture content. This study explores the primary factors that affect the yield of lipid extraction using Soxhlet, Randall and supercritical carbon dioxide (scCO2) extraction methods, with a particular emphasis on yield optimization for green extraction technologies (scCO2).RESULTSThe investigation revealed an increased lipid extraction yield for scCO2 from 7.4 for dry crushed stones to 20.6 g per 100 g dry weight when the cherry kernels are separated. The high initial moisture content affected all three extraction methods, but mostly impacted the scCO2 extraction, resulting in the co‐extraction of an aqueous phase. Lipid and aqueous yield could be manipulated by time, temperature and pressure. However, no observable influence on the composition of fatty acid methyl esters was detected.CONCLUSIONNumerous approaches are shown to enhance the lipid yield from cherry stone waste, depending on the desired outcome. When dealing with wet samples, Randall extraction proves to be the most effective method. On the other hand, scCO2 extraction presents distinct advantages, such as the extraction of food‐grade lipids and the co‐extraction of a unique aqueous phase, which comes at the expense of a reduced lipid yield. © 2024 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).