This study investigated the influence of shell microstructure on oil migration and fat bloom development in chocolate model systems. The microstructure of the model shells was varied by means of tempering or seeding cocoa butter and the addition of non-fat particles. Further, the impact of different storage conditions was studied. By using a set of novel analytical techniques the migration rate could be connected to the development of fat bloom at the surface. The non-seeded cocoa butter samples showed significantly higher rate of migration together with the highest rate of developed fat bloom, whereas the over-seeded cocoa butter samples showed low migration rate and low rate of fat bloom development. Addition of particles (sugar, cocoa powder and defatted cocoa powder) proved to have a significant impact on the microstructure, since these samples showed a substantially higher rate of migration and fat bloom development compared to seeded cocoa butter samples. Molecular diffusion could not explain the migration behaviour, thus, convective flow is suggested as an important contribution in addition to the molecular diffusion.