Agri-food supply chains have received the attention of many researchers in recent years for various reasons, including food security and health-related issues. Wheat, as a staple food in many countries, is the most cultivated crop in the world. Due to the importance of wheat, this paper proposes a mixed-integer linear mathematical model for redesigning and planning of the wheat supply chain. The proposed model determines the location and capacity of new storage facilities while addressing supplier selection, ordering, storing, transportation, and distribution problems. This model considers the differences between long-term and short-term storage facilities and the quality of wheat. Moreover, the proposed model addresses the uncertainties associated with the quantity of domestic supply and demand through a stochastic scenario-based programming approach. Applicability of this model is investigated using real data from the wheat supply chain of Iran. Results show that seven new long-term storage facilities should be opened, which decreases total costs by 3.45 percent.