In the present work, droplet-based microfluidics and sol-gel techniques were combined to synthesize highly monodisperse zinc oxide (ZnO) microspheres, which can be doped easily and precisely with dyes, such as rhodamine B (RhB), and whose size can be finely tuned in the 10–30 μm range. The as-synthesized microparticles were analyzed by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and confocal microscopy. The results reveal that the microspheres exhibit an excellent size monodispersity, hollow feature, and a porous shell with a thickness of about 0.6 μm, in good agreement with our calculations. We show in particular by means of fluorescence recovery after photobleaching (FRAP) analysis that the electric charges carried by ZnO nanoparticles primary units play a crucial role not just in the formation and structure of the synthesized ZnO microcapsules, but also in the confinement of dye molecules inside the microcapsules despite a demonstrated porosity of their shell in regards to the solvent (oil). Our results enable also the measurement of the diffusion coefficient of RhB molecules inside the microcapsules (DRhB=3.8×10−8 cm2/s), which is found two order of magnitude smaller than the literature value. We attribute such feature to a strong interaction between dye molecules and the electrical charges carried by ZnO nanoparticles. These results are important for potential applications in micro-thermometry (as shown recently in our previous study), photovoltaics, or photonics such as whispering gallery mode resonances.