This study aimed to investigate the untapped potential of seeds from Prunus avium, Prunus persica, and Prunus domestica for producing lipases and phospholipases. Using an orthogonal L9 design, it was determined that substrate concentration, incubation time, and agitation speed were the key factors influencing enzyme production. The optimal conditions for maximum enzyme yield were found to be a 10% substrate emulsion, 1-hour incubation, and an agitation speed of 4000 rpm, as identified through Taguchi methodology. ANOVA revealed that substrate concentration had the most significant impact (43.19%), followed by incubation time (28.16%) and agitation speed (28.65%). Under the optimized conditions, maximum enzyme activity was observed at pH 6 and 40°C for Prunus avium and Prunus domestica, while for Prunus persica, the optimal conditions were 45°C and pH 7. The enzymes extracted from Prunus persica seeds demonstrated the highest lipolytic activity, with lipase and phospholipase activities of 3.64 and 3.08 µU, respectively. These were followed by Prunus domestica (2.24 and 2.16 µU) and Prunus avium (1.52 and 0.80 µU), when tested in n-heptane solvent under the optimal conditions