This study was aimed at developing a sustainable versatile bio-based epoxy-silica material to be potentially employed as hydrophobic and biocidal consolidating product in the field of stone conservation. For this purpose, two hybrid formulations containing 2,2,4,4-tetramethyl-1,3-cyclobutanediol diglycidylether (CBDO-DGE), a cycloaliphatic epoxy precursor derived from the arnica root, together with (3-glycidyloxypropyl)trimethoxysilane (GPTMS) and octyltriethoxysilane (OcTES) as silica-forming additives, were chosen as the basis of the multifunctional material to be finely adjusted and gain biocidal properties. With this goal in mind, different synthetic strategies based on ionic liquids (ILs), essential oils (EOs) and nanoparticles (NPs) doping have been employed. Specifically, dimethyloctadecyl[3(trimethoxysilyl)propyl]ammonium chloride (QAS), tetradecyl phosphonium chloride (QPS) and thymol, as well as cerium-TiO2 NPs and thymol-loaded SiO2 NPs were incorporated into the starting hybrid formulations, during the sol-gel process, to investigate their influence on the network formation. First, distribution studies by scanning electron microscopy/energy-dispersive X-ray (SEM-EDS) analysis were performed, whereas the suitability of each formulation to match the main requirements for a stone conservation material was evaluated in terms of thermostability, hydrophobicity and inhibition of the microbiological growth by a combination of TG-DTA, DSC, dynamic mechanical analysis (DMA), with contact angle and disk-diffusion measurements, respectively. Based on the data analysis, it was observed that the direct incorporation of ILs and EOs had an adverse effect on the ability of GPTMS to act as a coupling agent. This resulted in decreased thermal stability and a 50 % reduction in glass transition temperatures, along with the retention of hydrophilic behavior. In contrast, the inclusion of NPs did not significantly interfere with the hybrid network formation, and effectively maintained the thermo-mechanical and hydrophobic properties of the hybrids within satisfactory parameters. Consequently, both nanocomposite materials were further tested on stone samples by artificial ageing experiments under acidic atmosphere. In view of the results, the hybrid enriched with thymol-loaded SiO2 NPs demonstrate the most suitable thermo-mechanical and hydrophobic properties (Tonset, Tα and CA values of 276 °C, 54 °C and 100°, respectively), as well as a proper biocidal capability against bacteria. Furthermore, the developed material provided effective stone protection, resulting in a 92 % reduction in material loss, while preserving the substrate chromatic characteristics (ΔE 2.23). These findings suggest that the proposed treatment meets the first main requirements for stone conservation.