A considerable fraction of the energy consumed in bread manufacturing is used for the baking process. A thorough understanding of internal moisture transfer mechanisms are important to optimise both the quality of the product and the economics of the process. From a transport phenomena point of view, bread baking has been considered as a simultaneous heat and mass transfer problem in a porous medium. Nevertheless, most efforts previously made have avoided modelling the phenomenon occurring in the microscale, although the mechanism occurs primarily in the microscale. In this work heat and moisture transfer models were developed to accomplish the mechanisms included, both in the microscale and the macroscale by means of Boltzmann’s equation. Modelling and predictions of moisture transfer, heat transfer, modelling of effective moisture diffusivity, thermal conductivity and diffusivity have been investigated in this work. The microstructure in the dough samples was obtained using micro-computer tomography images from the samples prior to baking. The models were quantified and validated with measurements from the literature in order to assess the predictive models. The simulated crust development has shown a crust thickness of 0.8 cm, which is slightly higher than similar experimental results in which a dehydrated thickness of 0.5–0.6 cm was reported. The crust over-estimation in this work fits to the overheating occurring in the model. Additionally, investigations were made on the influence of different porosities (11–16%) of the bread; the boundary layer temperature at a porosity of 11% was reached after 25 min and after 17.5 min at a porosity of 16%. Therewith, the results showed that, with increasing porosity, the heat transfer rate towards the centre was higher, which matches the knowledge of experienced bakers.