Designing an optimal risk-based monitoring plan for pathogens in the food industry is a complex process requiring careful consideration of multiple factors. This chapter outlines three key steps necessary for this endeavor. In situations where epidemiological, chemical, microbiological, or outbreak data is lacking, systematic identification of high-risk hazards and food products becomes challenging. This has led to the development of dedicated software tools to aid government food agencies in establishing effective risk mitigation measures. This chapter explores the features of the FDA-iRISK software, one of the prominent tools in this field, and provides specific examples for estimating and comparing the risks associated with foodborne illnesses arising from microbiological and chemical hazards. This software tool plays a crucial role in enhancing food safety and safeguarding public health in the food industry.