* Gas-filled intercellular spaces are considered the predominant pathways for gas transport through bulky plant organs such as fruit. Here, we introduce a methodology that combines a geometrical model of the tissue microstructure with mathematical equations to describe gas exchange mechanisms involved in fruit respiration. * Pear (Pyrus communis) was chosen as a model system. The two-dimensional microstructure of cortex tissue was modelled based on light microscopy images. The transport of O(2) and CO(2) in the intercellular space, cell wall network and cytoplasm was modelled using diffusion laws, irreversible thermodynamics and enzyme kinetics. * In silico analysis showed that O(2) transport mainly occurred through intercellular spaces and less through the intracellular liquid, while CO(2) was transported at equal rates in both phases. Simulations indicated that biological variation of the apparent diffusivity appears to be caused by the random distribution of cells and intercellular spaces in tissue. Temperature does not affect modelled gas exchange properties; it rather acts on the respiration metabolism. * This modelling approach provides, for the first time, detailed information about gas exchange mechanisms at the microscopic scale in bulky plant organs, such as fruit, and can be used to study conditions of anoxia.