The agricultural sector contributes fourteen percent to the Philippines' gross domestic product; however, the country’s staple food requirement is still insufficient as data show a 16.4% loss in the post-harvesting process of rice crops due to the conventional way of harvesting. The purpose of this study is to provide an optimized process flow model that will lessen the loss incurred in the agro-food supply chain process. Literature reviews were done to validate the gathered data among government agencies, and through the use of Analytical Hierarchy Process (AHP), key variables were identified in determining the relative weights and criteria fitted in the model. Results show that type of seeds, timely harvest, temperature management, moisture content, and ethylene production are relevant factors that cause food loss in the agro-food supply chain. The recommendation includes the establishment of an integrated internet of things (IoT) process incorporating the key variables beneficial for the stakeholders.