The elaboration of nanostructures including both functional materials and functional morphology is a crucial scientific and technological challenge. In this work diatom frustule replicas mainly consisting of magnesium silicon nitride and nanocrystalline silicon have been obtained by simultaneous metallothermic reduction and nitriding of silica diatom frustules at 800 °C. The frustule replicas retained most of the complex nanoporous structures from the original frustules in the conversion. The optical scattering, transmittance and luminescence properties of the replicas have been investigated. Luminescence was observed and attributed to the presence of silicon nanocrystals. Wavelength dependent diffraction of light was observed in bio-silica frustules but not in frustule replicas, this was attributed to surface coarsening of the replicas during reaction. Light transmittance was found to be lower in frustule replicas and was consistent with absorption of light by Si nanocrystals.