Siliceous diatom frustules represent an up-and-coming platform for a range of bio-assisted nanofabrication processes able to overcome the complexity and high cost of current engineering technology solutions in terms of negligibly small power consumption and environmentally friendly processing combined with unique highly porous structures and properties. Herein, the modification of diatomite – a soft, loose, and fine-grained siliceous sedimentary rock composed of the remains of fossilized diatoms – with gold nanoparticles using layer-by-layer technology in combination with a freezing-induced loading approach is demonstrated. The obtained composite structures are characterized by dynamic light scattering, extinction spectroscopy, scanning (SEM) and transmission electron microscopy (TEM), and photoacoustic imaging techniques, and tested as a platform for surface-enhanced Raman scattering (SERS) using Rhodamine 6G. SEM, TEM, and energy dispersive X-ray spectroscopy (EDX) confirmed a dense coating of gold nanoparticles with an average size of 19 nm on the surface of the diatomite and within the pores. The photoacoustic signal excited at a wavelength of 532 nm increases with increasing loading cycles of up to three polyelectrolyte-gold nanoparticle bilayers. The hybrid materials based on diatomite modified with gold nanoparticles can be used as SERS substrates, but also as biosensors, catalysts, and platforms for advanced bioimaging.