Complex silica-based microcapsules with nanopatterned features were made using Pickering stabilization as a fabrication tool. A sequential two-step liquid-liquid interface-driven assembly process was employed using Laponite clay discs and Laponite armored polystyrene latex particles as solids to stabilize emulsion droplets on two different length scales. The discotic Laponite particles and poly(diethoxysiloxane) were used as silica sources. The ethoxy groups of the poly(diethoxysiloxane) were removed via a triethylamine-catalyzed interfacial hydrolysis and sol-gel reaction. The organic components were removed via a calcination step. The two-stage templating route provided siliceous microcapsules of which the capsule walls were decorated on either the outside or inside with nanocapsules composed of Laponite clay.