Proteins are vital to the diet. To reduce the climate impact of foods, which generates one-third of human-caused greenhouse emissions, the transition from meat-based to alternative proteins is accelerating. For all foods, prolonging shelf-lives is necessary, which requires reducing the water activity through processes like evaporation. To avoid triggering protein-based food allergy during and improve the efficiency of food processing, the understanding of changing protein conformations caused by processing conditions is imperative. Such molecular-level resolution is challenging experimentally, but readily facilitated by molecular dynamics (MD) simulations, which have been invaluable for fields like drug efficacy, but not yet been fully exploited for food protein processing. Leveraging the applicant’s expertise in MD simulations and chemical process engineering, the proposed research aims at fundamentally understanding protein behaviours during falling-film evaporation (FFE), which is commonly used for thermal-sensitive foods (e.g., milk). A multi-pronged approach is proposed: (1) understand protein fouling behaviours, which is the progressive build-up of protein deposits that reduces the de-watering efficiency; (2) understand the impact of thermal stressors on the molecular structures of food proteins; and (3) bridge molecular- and continuum-scale simulations via the shear-viscosity relationship. The results are valuable for advancing the green transition of the food industry.