The microstructure of chocolate model systems was investigated at the meso (~. 10. μm), micro (~. 50. μm), and macro (0.1-1 mm) scales simultaneously, to examine effect of pre-crystallization process and/or solid particle addition on the formation of a dense structure. The structure density was quantified by measuring the diffusion rate of small molecules at different length scales. At the meso scale, fluorescence recovery after photobleaching (FRAP) was utilized to quantify local diffusion rate solely in the fat phase, whereas high-performance liquid chromatography (HPLC) measurements were made to assess the global diffusion of the same molecules at the macro scale. Both techniques were used in combination with microstructure characterization using confocal laser scanning microscopy (micro scale) and supported by differential scanning calorimeter melting curves for estimating cocoa butter polymorphism. Both FRAP and HPLC analysis generated relevant information on the effect of pre-crystallization and solid particle addition on the structure density. FRAP measurements gave detailed information on microstructure heterogeneity or homogeneity in the cocoa butter, whereas HPLC clearly revealed the impact of solid particles on the structure density. Combining the two techniques revealed that a compact and homogeneous structure obtained through optimized pre-crystallization is required at all times, i.e., immediately after cooling and throughout the product's shelf life, to retard global diffusion in confectionery systems.