Some food pathogens are not well controlled by lethality treatments followed by refrigeration. A food processing facility according to this invention reduces the likelihood that food pathogens will be able to enter the food processing facility, or spread should they be able to enter. The food processing facility is divided into a plurality of area, with different areas having different allowed actions that can be taken on the food product, different rules and/or procedures for persons who are allowed entry, and/or different levels of cleanliness. The food processing facility includes a plurality of separate rooms for processing the food product, each including separate food processing machines, air handling systems, drain systems and/or often-used supplies and tools. Different air pressures within different areas limit the possible movement of airborne food pathogens. Sanitizing stations are placed between various ones of the different areas.