Pasteurization of crushed tomato in glass bottles was evaluated using a multiphysics model, aiming to understand the temperature profiles and quality losses during the heating and cooling stages of the process. In order to rigorously simulate the pasteurization process, a finite element model was built using experimentally measured product and heat transfer parameters (thermal conductivity, density, specific heat, and convective heat transfer coefficient) and the kinetics of thermal degradation of the quality parameters (color, lycopene and ascorbic acid). The developed model was successfully validated by considering both the temperature profile (R 2 = 0.99) and quality losses (relative differences <10%). After validation, equivalent thermal processes were simulated at three temperatures (80, 90 and 100 °C). Numerical results revealed that the process at 100 °C provided the best retention of quality compared to the 80 and 90 °C processes. For the three quality parameters evaluated, color ( a* value), lycopene and ascorbic acid, for 100 °C, retention values of 92.25, 74.76 and 83.68% were obtained, while for the 80 °C treatment, the retentions were 65.60, 18.35 and 36.13%, respectively. • A multiphysics model was built to study crushed tomato in glass bottle pasteurization. • The microbial inactivation during cooling was greater than 50% of the total P-value . • Coldest point was located on axial axis at 38.5% of the total height for all cases. • The best retention of quality was provided by the treatment at 100 °C. • The developed model can be used to design and optimize protocols for pasteurization.