Agricultural activities have adverse effects on the environment by emitting greenhouse gases and consuming great deals of freshwater. In addition, fruits constitute a substantial part of agricultural products used for balancing diets. In particular, pomegranate is one of the most used products by people of different cultures. In this study, a multi-objective mathematical model is developed to balance sustainability dimensions by focusing on selecting the optimal cultivation process and determining the optimal material flows between pomegranate supply chain facilities. The proposed model maximizes the total profit and the number of created job opportunities due to cultivation process selection and the establishment of plants. It also addresses the environmental impacts by minimizing fertilizer, pesticide, and water consumption in pomegranate cultivation. The model also considers the reverse flow of pomegranate peel and seeds to recapture the value of these products, commonly known as waste. A real case in the Mazandaran province of Iran is considered for validating the developed model. Finally, comprehensive sensitivity analyses are performed on the influential factors of the problem, and managerial implications are presented.