We have investigated the feasibility of a new two-step protocol for the restoration of marbles. The process employs a polyelectrolyte multilayer film that enhances the chemical affinity between the treated stone and restorative material (hydroxyapatite nanocrystals), through functionalization, while at the same time it attributes an acid resistant property to the resulting system. Surface functionalization and material deposition is achieved through spraying; a simple and versatile application method suitable for objects of various sizes and geometries. Polyelectrolyte (polyethylenimine and polyacrylic acid) deposition was examined through Attenuated Total Reflection Fourier-Transform Infrared Spectroscopy (ATR-FTIR) and Atomic Force Microscopy (AFM), and tested through contact angle, water absorption and dissolution experiments. The hydroxyapatite nanocrystals were studied by ATR-FTIR, z-potential, AFM and Scanning Electron Microscopy (SEM), and characterized via contact angle and color alteration measurements. Our results show that the polyelectrolyte multilayer was stable in an aqueous environment with increased acid resistance (up to 46% decrease in mass weight loss when compared with untreated samples) and decreased water absorption (up to 39%). Color measurements of the outer hydroxyapatite layer showed a minimal color alteration for one type of the tested substrates showing low color difference values (ΔΕ* < 5). The results suggest that the proposed method holds great potential for marble restoration as it attributes multi-functionality and is easy to apply.