Fungal biosynthesis of nanoparticles is considered an eco-friendly and safe tool for the synthesis of nanoparticles applied in various fields. In this work, iron oxide nanoparticles were biosynthesized by fungi isolated from fungal attacked archaeological cartonnage and used to clean deteriorated cartonnage. Six fungal strains were isolated and molecularly identified. These identified fungi were used for the biosynthesis of nanoparticles of iron oxide from both ferrous sulfate and ferric chloride. The most appropriate nano-particles for cleaning artworks were produced from Penicillium commune MH5. Iron oxide nanoparticles were characterized using colorimeter, Ultraviolet-visible spectroscopy, X-ray diffraction, and Transmission electron microscope studies. Iron nanoparticles were added to magnetic nano gel, microemulsions micelles solutions (Oil in water microemulsion made with sodium dodecyl sulfate (SDS), 1-pentanol (PeOH) as co-surfactant, propylene carbonate (PC), pure ethyl acetate are replaced by less toxic solvents), and compared with nano gel which uses in cleaning cartonnage which fungi isolated from it. The Fourier transform infrared spectroscopy, scanning electron microscopy, and coloring measurement was used to evaluate the successful effect of the new gel with the magnetic nanoparticles in cleaning the artwork surfaces.