This study introduces a novel approach to synthesising a three-dimensional (3D) micro-nanostructured amorphous biosilica. The biosilica is coated with cerium oxide nanoparticles obtained from laboratory-grown unicellular photosynthetic algae (diatoms) doped metabolically with cerium. This unique method utilises the ability of diatom cells to absorb cerium metabolically and deposit it on their silica exoskeleton as cerium oxide nanoparticles. The resulting composite (Ce-DBioSiO2) combines the unique structural and photonic properties of diatom biosilica (DBioSiO2) with the functionality of immobilised CeO2 nanoparticles. The kinetics of the cerium metabolic insertion by diatom cells and the physicochemical properties of the obtained composites were thoroughly investigated. The resulting Ce-DBioSiO2 composite exhibits intense Stokes fluorescence in the violet–blue region under ultraviolet (UV) irradiation and anti-Stokes intense violet and faint green emissions under the 800 nm near-infrared excitation with a xenon lamp at room temperature in an ambient atmosphere.