One of the challenges within nanoscience is the formation of nanoparticles of a consistent size, shape, and spatial arrangement. One solution to this problem is to incorporate guest molecules into larger hosts for confined nanoscale synthesis. The central theme of this thesis is the formation of novel nanocomposites using this host-guest approach. Cross-linked tetragonal lysozyme crystals and hydrophobic 2:1 phyllosilicate clays were utilized as the host materials for the synthesis of nanostructured arrays, and were characterised using optical microscopy, SEM, TEM, EDX, FTIR, UV-vis and TGA. Tetragonal lysozyme crystals were grown, cross-linked, and characterised before being infiltrated with various precursors. An oxidising agent was infiltrated along with heterocyclic monomers to form high aspect ratio wires of the conducting polymers polypyrrole and polyaniline. Cross-linked lysozyme crystals were also used for the deposition of arrays of plasmonically active gold and silver, by chemical and photoreduction, respectively. The internal metallic structure of the protein/metal composites were then modelled using advanced UV-vis and fluorescence spectroscopy to reveal the presence of prolate spheroidal nanoclusters. Finally, microwave-assisted pyrolysis was used to synthesise intracrystalline arrays of highly fluorescent nanoscale carbon dots from a precursor solution of citric acid and ethylene diamine. The carbon nanostructures could be released from the protein crystals via treatment with a solution of sodium borohydride, and could also have their fluorescence emissions tuned by infiltration of fluorescent dye molecules. Finally, three novel 2: 1 phyllosilicateorganoclays were synthesised with pendant propyl, octyl, and octadecyl chains using a one-step sol-gel method. The octyl clay was used to accommodate a palladium (11) complex that was subsequently reduced into Pdo nanoparticles within the clay structure. All of the clays and the clay/nanoparticle composite were found to be hydrophobic, and could be exfoliated in toluene to form water-in-oil Pickering emulsions, which were chemically crosslinked to form colloidosomes