Human pathogens interact with fresh produce through the initial attachment, internalization, growth/death, spreading, and dispersion. In order to develop better mitigation strategies for improving fresh produce safety, physics-based models were developed to provide a mechanistic understanding of experimental results in literature that extrapolate between food systems, improving food safety predictions and process safety. Non-invasive imaging, magnetic resonance imaging (MRI) and X-ray microcomputed tomography (X-ray [MICRO SIGN]CT), was used to determine model properties, acquire geometries, and validate results. Three models were then developed: a porous media transport model to study internalization of pathogens during hydrocooling, a two-way coupled continuum-individual based model to study growth, death, and dispersion on leafy greens, and a Lagrangian particle tracking model for bacteria to study how plant surface microstructures affect their attachment. The models are connected through the numerical procedures, i.e. multiscale modeling, and theoretical framework in each. Each model works across time and length scales to develop the computational, multiscale modeling foundation for elucidating the physical mechanisms of fresh produce contamination by bacteria to better develop mitigation strategies.