Perilla seed meal (PSM) is a by-product rich in proteins and bioactive compounds obtained by cold pressed oil extraction method. Microwave is an efficient nonconventional technology usually used to accelerate the recovery of the extracts. In this study, pH, microwave power and treatment time were optimized to maximize the recovery of targeted compounds using Box–Behnken design. The pH was found to be the most significant variable affecting the yield followed by microwave power and treatment time (based on F-value). Compared to conventional alkaline extraction, an increase in the yield of protein content by 10.58%, antioxidant activity by 7.48% and total phenolic content by 21.59% was recorded at the optimal values of pH (11.5) microwave power (160 W) and treatment time (30 s). Moreover, principle component analysis revealed opposite correlation between antioxidant activity and extraction of protein/phenolics suggesting the loss of bioactivity at the higher yield of extracts. Also, from the clustering analysis, the effect of microwave treatment found to be lower in more extreme alkaline conditions compared to lower pH values. Hence, lower alkaline conditions are suggested for the microwave treatment to develop better control system in the extraction industry. Plant extracts are frequently obtained using microwave-assisted extraction (MAE) Alkalinity level, microwave power and exposure time were analyzed Multicomponent analysis revealed optimum microwave treatments at less alkaline conditions The protein yield was 10.5% higher while total phenolic content was 21.6% higher than conventional alkaline extraction in optimum microwave conditions The MAE is recommended to obtain a high recovery of extracts with minimum degradation [ABSTRACT FROM AUTHOR]