Microbiological Risk Assessment (MRA) is a structured process for determining the public health risk associated with foodborne pathogens. In recent years, there has been a strong tendency in providing food safety decisions based upon quantitative assessment. Especially, variability and uncertainty inherent to biological processes have been integrated in food safety management through the use of powerful statistical and probabilistic techniques. Besides, recent developments in omic technologies may fill knowledge gaps on strain diversity and physiological variability, and, open new perspectives to refine hazard identification. Last, to satisfy the societal demand for balanced recommendations on food, MRA could be, in a near future, embedded into a more comprehensive assessment including chemical and nutritional issues, but also, cost and sustainability considerations.