National governments are moving to integrate risk analysis frameworks into food safety management systems at the country level. However, this process is less advanced in developing countries. In this context, the Chilean Livestock and Agriculture Service (SAG), Food Quality and Safety Agency (ACHIPIA) and the University of Nebraska-Lincoln (UNL) collaborated on a project to control generic Escherichia coli and Hepatitis A virus (HAV) contamination in both fresh and frozen raspberry products destined for export. The objectives of this study were to 1) identify along the raspberry supply chain the most influential factors of E. coli and HAV contamination in the final products; and 2) evaluate the efficacies of possible interventions to control these influential factors. To achieve these objectives, a unified quantitative model of microbial contamination in raspberries was developed to describe the impact of factors in a continuum from the farm to the destination of importation on E. coli/HAV contamination in fresh and frozen raspberry products. Multiple surveys were conducted to obtain country-specific data on current common practices of producing and processing raspberries in Chile for inputs into the simulation model. The model estimated mean bacterial loads of −1.64 and −5.46 logCFU/g for E. coli and mean viral loads of −6.45 and −6.51 logPDU/g for HAV in fresh and frozen raspberries, respectively. Sensitivity and scenario analyses indicated that reduction of E. coli contamination in the end products can be effectively achieved by improving the quality of water used for pesticide application, as well as by controlling the transport and storage time and temperature along raspberries supply chain. By contrast, to control HAV contamination in the end products, efforts should be focused on improving the hygiene practices of berry handlers on the farm and at the packing plant. This project provides straightforward recommendations for Chilean food safety authorities to effectively prioritize their financial and human resources to proactively prevent microbial contamination in raspberries. Moreover, this project provide a framework that can be extended to other countries to promote capability building for applying risk-based food safety management systems for public health protection.