Evaporation induced assembly of colloidal particles in an aerosol droplet has been utilized to synthesize nano-structured porous silica microcapsules comprising of interlocked correlated nano-particles. Morphology of the microcapsules was tuned by controlling the rate of evaporation. In the present work, we demonstrate that such porous capsules can efficiently take up cationic dye from aqueous solution. In-situ UV–vis spectroscopy has been utilized to monitor the time dependence of sorption by these capsules. Small-angle X-ray scattering and scanning electron microscopy have been used to probe the multi-level structure of the powder granules. Thermal analysis was performed on the dye-sorbed granules to investigate the effect of confinement on the thermal degradation behaviour of the dye molecules within the granules.