Mycelium derived from Ganoderma lucidum was employed as a template for synthesising silicon oxide (SiOx) nanofibers. The intricate structures of mycelial hyphae fibrils were replicated with high precision using an inexpensive commercial silane (3-aminopropyl)-triethoxysilane (APTES). Following the removal of the organic mycelium template phase at 600 °C, APTES was successfully converted to SiOx. The resulting SiOx fibres retained the morphology of the mycelium template, with a nearly identical fibre density to the original fibrous network. A fibril diameter reduction of approximately 43% was observed from 603 to 344 nm. All synthesised materials exhibited coherent structural integrity, sufficient for handling without breakage, although they were notably less mechanically flexible than the original mycelium template. The novel hybrid mycelium-3-aminopropyl-silsesquioxane fibre network and the thermally converted SiOx network displayed notable liquid absorption properties. These materials allowed for the preferential absorption of oil or water, depending on the presence of the amino group functionality. Remarkably, the SiOx network rapidly absorbed methylene blue-dyed water within 400 ms, demonstrating behaviour opposite to the virgin mycelium network. Additionally, the materials exhibited high thermal stability, withstanding flame exposure at approximately 1400 °C while maintaining their nano/micromorphology. This innovative approach of using “living” templates expands the range of morphologies that can be replicated in inorganic materials, enabling the creation of genetically and environmentally tuneable structures. The SiOx nanofibers produced through this method have potential applications in various fields, including water purification, biosensors, catalytic support, and insulation.