Micro-aeration is a method to modify the sensorial attributes of chocolate but also affects the material properties of chocolate, which in turn, determine its material response during manufacturing and oral processes. This study aims to define the effect of micro-aeration on the thermal properties of chocolate by considering the changes of chocolate microstructure due to micro-aeration. Micro-aeration was found to alter the chocolate microstructure creating a layer of a third phase at the porous interfaces, which is argued to consist of cocoa butter of higher melting properties. A multiscale Finite Element Model is developed, which was confirmed by macroscale heat transfer measurements, to parametrically simulate the structural changes of micro-porous chocolates at the microscale level and estimate their effective properties, such as thermal conductivity and specific heat capacity. The developed multiscale computational model simulates the porous chocolate as a two-phase (chocolate- pores) or three-phase material (chocolate-cocoa butter layer- pores). The investigation identified a new, complex transient thermal mechanism that controls the behaviour of micro-aerated chocolate during melting and solidification. The results showed a maximum 13% reduction of keff and 15% increase of Cpeff with 15% micro-aeration resulting to a slower transient heat transfer through the micro-aerated chocolate. The reason is that the micro-aerated chocolate can store a larger amount of thermal energy than its solid counterpart. This effect slows down the transient heat transfer rate in the chocolate and modifies melting/solidification rate and impacts sensorial attributes during oral processing and cooling during manufacturing.