Citrus supply chains (CSC) are increasingly important in research due to high loss and waste, increasing demand, wide application for other industries, and differences in CSCs from country to country. This study proposes a new structure for CSC by introducing collection points to collect citrus from the farms in Jordan Valley and transport it to a citrus hub responsible for receiving, packaging, and transporting the citrus to distribution centers. The objective of this structure is to minimize the loss and waste and provide a new supply chain (SC) with stable infrastructure to track citrus from the initial stages and implement technologies such as the Cold SC. Therefore, it is crucial to find the optimum number of collection points, citrus hubs, and locations based on carbon footprint and transportation costs. The model introduced was solved using Open Solver Adds-ins after collecting data such as distances and coordinates using Google Maps and the altitude of those coordinates from SolarGIS. After running the model, it was found that the optimum number of collection points is 52 and the optimum number of citrus hubs is two. The results showed that the transportation costs of one hub are lower by 30%, whereas for two hubs are lower by 60% compared to the current location of the central market of fruits and vegetables (CM). The “kg CO₂ e/kg citrus” values are 0.48 and 0.24 for one hub and two hubs, respectively, which showed a significant reduction compared to CM, which was 0.69 kg CO₂ e/kg citrus. Therefore, installing two citrus hubs will improve the overall sustainable performance of CSC. Future research might be directed to integrate the circular economy into CSC and find possible applications for citrus loss and waste.