In the context of a growing world population and the need to use limited resources responsibly, this study is motivated by the increasing pressures on the food industry, which include issues of food security, safety, and waste. In the context of a global food supply chain, we combine processing time and cost (PT&C) with operational risk (ORk) in a novel integrated approach to designing and optimizing monitoring systems. This study of a flagship product widely consumed around the world provides quantitative analysis and results based on real-world data from an international food company. The findings indicate that our multi-objective methodology provides quantitative insights into—and is capable of quantifying—an unexpected nonlinear relationship between PT&C and ORk. We show numerically how to decrease PT&C significantly by means of a minor increase in ORk, an outcome which is highly appealing for the industry. In addition, we provide accurate measurements of the impact of each individual monitoring activity, which allows the identification of the monitoring activities that are most critical. Generalizable insights for practitioners are derived from a step-by-step optimization of the entire monitoring system.