In this study, colloidal clusters decorated with fluorescent dyes were fabricated by evaporation-driven self-assembly using emulsion droplets as confining geometries. Silica microspheres were synthesized by Stober method followed by the modification with dye molecules through additional surface sol-gel reaction for the formation of thin silica shell. The surface of the resultant dye-doped silica microspheres was modified with hydrophobic silane coupling agent to disperse the particle suspension in organic solvent such as hexane. The fluorescent silica microspheres were self-assembled inside oil-in-water emulsions by evaporation-driven self-assembly for the formation of colloidal clusters, potentially applicable for photonic molecules. The clusters with fluorescent emission were observed using confocal microscope.