Convective cooling is essential in many supply chain unit operations for refrigerated transport and cold storage of fresh products. Fruit must be kept at low temperatures to preserve quality and to slow down biochemically-driven food degradation. Along the cold chain, heterogeneities in temperatures are present among individual products, which influence the resulting product quality, causing significant food losses. This study presents a thermo-fluid dynamic model of a single mango fruit to better understand the convective cooling behavior of fruits with more complex, non-spherical shapes and a heterogeneous composition. To explain the biochemical and biological processes affecting the product's final quality, experimental data from the literature are used to calibrate kinetic rate laws for the prediction of different quality attributes (overall quality, flesh firmness, titratable acidity, total soluble solids and vitamin content) over time.The accuracy of airflow modeling and of applying a realistic fruit shape are assessed. It is quantified how much higher airspeeds lead to faster cooling of the pulp and seed, and how strong non-uniform temperature heterogeneities are inside the fruit. From sensitivity analysis, air temperature has the most impact on fruit temperature during cooling, while thermal properties and fruit size have a minor influence. The evolution of the quality attributes is shown at different temperatures, and the heterogeneities in quality within the mango fruit are also investigated. The obtained insights will help advance cooling process optimization for other complex-shaped, multi-material fruit and vegetables.