The study was applied to fresh tomatoes (Solanum Lycopersicum, Marbone variety). First, a field survey was conducted to obtain statistical data on the temperature and duration (minimum, mode, maximum) at different stages in the supply chain. Then, the physicochemical, phytochemical and volatile compounds were measured at harvest and on five different days (3, 7, 11, 14 and 21 days) for two maturity stages at harvest (green-orange and light red) and under three storage temperatures (3 °C, 8 °C and 15 °C). These data were used to evaluate the combined impact of harvest maturity, time and storage temperature on the evolution of the different compounds. From the same data, quality models were developed based on the Arrhenius equation to describe the tomato quality evolution under different storage temperatures for (Z)-3 hexenal, total sum of acids, lycopene and chlorogenic acid. These compounds were chosen because of their relation to commercial and nutritional qualities. The model results were validated using additional data from a different study conducted on one constant temperature profile and two dynamic time-temperature profiles as in a supply chain. Finally, data from the field survey and the quality models were combined in a Monte Carlo process (105 product items) to simulate the variability of time-temperature profiles from the grower to the sales outlet and its impact on the quality attributes. For two maturity stages at harvest, the impact of the supply chain on the quality attributes of tomatoes at the sales outlet was also analyzed. Simulation results show that that the maturity stage at harvest significantly impacts the final lycopene content and the total sum of acids in tomatoes at the sales outlet, with fruit harvested at the light red stage containing higher lycopene levels (and a lower hue angle) and a lower total sum of acids in comparison with fruit harvested at the green-orange stage. However, at the sales outlet, the concentrations of chlorogenic acid and (Z)-3-hexenal in fruit harvested at the green-orange and light red stages are similar. This information would be useful for fruit and vegetable stakeholders for time-temperature management of tomato fruit throughout the supply chain in order to optimally preserve the main quality attributes.