The effective diffusivity is a key engineering property of fruit that affects transport of metabolic gases and, hence, ripening. It strongly depends on the microstructure of the fruit. In bulky fruit such as tomato, porosity and pore structure differ between tissues and change during maturation and ripening. Knowledge of the relationship between gas diffusivity and microstructure of tomato will aid management and control of postharvest operations. By using mathematical models of mass transport that incorporate the 3-D microscopic tissue geometry obtained from micro-computed tomography (μ-CT), the relationship between microstructural features and gas diffusivity may be computed in a direct way. In this study, a previously validated pore-scale network model (PNM) was used to simulate the effective gas diffusivity of O2, CO2 and ethylene for five types of tomato fruit tissues (i.e., outer mesocarp, inner mesocarp, septa, placenta and columella) at different maturation and ripeness stages. The effective gas diffusivity of the placenta and columella was large during the entire ripening process as these tissues contained more interconnected open intercellular spaces. The effective diffusivity of the inner mesocarp increased with increasing porosity during ripening while the microstructural changes of the outer mesocarp lagged compared to those of the inner mesocarp region, resulting in a delayed increase of the effective gas diffusivity with ripening. Regression models between the effective diffusivity of O2, CO2 and ethylene as a function of porosity, open porosity or tortuosity were established. This study provides a quantitative basis for further gas exchange modeling in intact tomato fruit to predict their ripening process.