Governmental food safety monitoring is moving towards risk-based monitoring. Three steps are needed to design an optimal risk-based monitoring plan for pathogens. First pathogen-product combinations need to be ranked, according to their probability of contamination of the sampled product, consequences to human health, or the combination of one or more of these aspects. Second, food business operators (FBO) that will be sampled need to be selected. FBOs can be selected based on historical data but also on socio-economic factors. These include both internal factors, such as the company size, the perception of the likelihood and the consequence of producing unsafe food, the social pressure, as well as external factors, such as the legislation in place, or the budget available. Third, for the selected pathogen-product combinations and FBOs, an optimal sampling strategy needs to be determined. The optimal number of lots to be sampled and the optimal number of samples per lot depend on the prevalence of the pathogen, the distribution of the pathogen between and within lots, and the available resources. Furthermore, the sampling strategy in terms of where and how the samples need to be collected from the lot is relevant to define. To the best of our knowledge, the three steps to design an optimal risk-based monitoring plan for microbiological hazards, as proposed in this study, have not yet been considered together. This study thus provides a basis to further optimize the risk-based monitoring process.