Multiple triphasic emulsions constitute versatile templates for the preparation of complex particles and capsules. In these emulsions the volume fractions and interfacial tensions between the phases dictate the droplet morphology, enabling various morphologies such as Janus, core-shell and snowman droplets. In this article, we describe the preparation of all-aqueous water-in-water (W/W) emulsions composed by a perylene-based chromonic liquid crystal and a hydrophilic polymer. This combination yields emulsions with liquid crystalline droplets exhibiting diverse configurations of the director, including the formation of twisted structures, from achiral mesogens. Three-phase multiple emulsions with various morphologies were obtained by the emulsification of W/W emulsions in either another aqueous phase or in hexadecane. The resulting droplet morphologies depended on the composition of the system. Furthermore, hollow silica particles with a chromonic-templated microporous structure were prepared via a sol−gel reaction within the liquid crystalline phase of water-in-water-in-oil emulsions. These findings show how the unique templating properties of chromonic liquid crystals can be applied to all-aqueous emulsions for the synthesis of complex silica particles, with a controlled structure both at the micro- and nanoscale.