This study evaluates a SiO₂ nanoparticle (SiO₂NPs)/Paraloid B-72 nanocomposite as a restorative and antifungal treatment for deteriorated sandstone at the Ptolemaic Temple of Isis, located within a densely populated residential area. The temple stones exhibit structural damage, soiling, and severe microbiological deterioration. Fungal isolates from the sandstone were cultured on PDA medium and identified by ITS region DNA sequencing as Alternaria alternata, Penicillium chrysogenum, and Aspergillus niger. The SiO₂NPs and their Paraloid B-72 nanocomposites were synthesized and characterized using transmission electron microscopy (TEM) and X-ray diffraction (XRD). Stone samples, examined before and after treatment via SEM-EDX, TEM, and XRD, were used to assess both conservation performance and compatibility. Laboratory antifungal tests showed that SiO₂NPs at 300 ppm exhibited the greatest inhibition of mycelial growth, reaching 91.59% for P. chrysogenum, 90.77% for A. niger, and 85.2% for A. alternata. Mechanical testing demonstrated that treatment with the SiO₂NPs/Paraloid B-72 nanocomposite enhanced stone strength, increasing compressive strength from 26.5 MPa to 27.4 MPa. SEM images confirmed excellent, homogeneous dispersion of the nanocomposite on stone grains, forming a coherent coating without pore occlusion. Overall, the SiO₂NPs/Paraloid B-72 formulation improved sandstone surface properties while substantially improving short-term mechanical performance and antifungal efficacy, indicating promise for enhancing restoration procedures when combined with established conservation protocols for sandstone architectural heritage.