Controlled release of food ingredients and their protection from oxidation are the key functionality provided by microencapsulation. In the present study, pomegranate seed oil, rich in conjugated linolenic acid, was microencapsulated. As encapsulating agent, sodium alginate or trehalose was used. Calcium caseinate was used as the emulsifier. Performances of the two encapsulants were compared in respect of the rate of release of core material from the microcapsules and stability of microcapsules against harsh conditions. Microencapsulation was carried out by preparation of an emulsion containing calcium caseinate as the emulsion stabilizer and a water-soluble carbohydrate (either sodium alginate or trehalose) as the encapsulant. An oil-in-water emulsion was prepared with pomegranate seed oil as the inner core material. The emulsion was thereby freeze-dried and the dried product pulverized. External morphology of the microcapsules was studied under scanning electron microscope. Micrographs showed that both types of microcapsules had uneven surface morphology. Release rate of the microcapsules was studied using UV-spectrophotometer. Trehalose-based microcapsules showed higher release rate. On subjecting the microcapsules at 110 °C for specific time periods, it was observed that sodium alginate microcapsules retained their original properties. Hence, we can say that sodium alginate microcapsules are more heat resistant than trehalose microcapsules.