A method and system is provided whereby pathogens in food are reduced by first sealing food in a package and then applying high hydrostatic pressure to the sealed package. The package is moved to a clean area having pathogen-reducing treatment such as a cleansing plasma. The food is removed from the sealed package and then transferred to a food processor such as a grinder or dicer having internal pathogen reducing treatment. The food may then be transferred to a patty maker having internal cleansing plasma. The food may then be transferred to a freezer or freeze dryer having internal cleansing plasma.