Custard apple (Annona Squamosa) seed is mainly an agricultural waste generated in many fruit and pulp industries. The seeds are an important source of value added products such as oil, polyphenols, and acetogenins, possessing medicinal properties and having excellent market potential. The current work aims at developing an intensified method to extract volatile and non-volatile components from custard apple seeds using supercritical CO2 extraction (SC-CO2) with detailed process optimization so as to establish conditions for maximum yield. The maximum extraction of non-volatile components was obtained at optimized conditions of 25 MPa pressure, 318 K temperature, and 2.5 mL/min flow rate. The extraction of volatile oils was maximum under conditions of 15 MPa pressure, 308 K temperature, and 1.5 mL/min. The extraction was observed to be complete within 1 h due to an increase in permeability based on the action of high pressure SC-CO2, as also evident from the results of scanning electron microscopy (SEM) imaging. The antibacterial and antifungal properties of the obtained extract were also demonstrated in the work. The total number of energy units required for 1 kg extract production was calculated to be 40.69 kW h.