In order to protect a material belonging to Cultural Heritage (i.e., stone, wood) from weathering, and in turn to preserve its beauty and historical value for the future generations, the contact with external harmful agents, particularly water, must be avoided, or at least limited. This task can be successfully obtained with the use of a protective organic coating. The use of nano-metric reinforcing agents in conventional polymeric coatings demonstrated to be a successful route in achieving better protective performance of the films and improved physical properties, even in extreme environments. The present paper would, therefore, review the more recent findings in this field. Generally speaking, when a hydrophobic product is applied on its surface, the stone material will absorb less water and consequently, less substances which may be harmful to it. An efficient organic coating should also supply wear and abrasion resistance, resistance to aggressive chemicals, excellent bond to the substrate; finally, it should be also able to guarantee vapor exchange between the environment and the material interior, i.e., the material should keep the same water vapor permeability as if it was un-protected. To regard to the conservation of wood artifacts, protective treatments for wood will preserve the material from environmental agents and biological attack. Hence, potential advantages of hybrid (organic–inorganic) nano-composite coatings for stone/wood have been found to be: Enhanced mechanical properties in comparison to the pure polymeric matrix, due to the reinforcing effect of the nano-filler; superior barrier properties (the presence of the nano-filler hinders the ingress of water and/or potentially harmful chemicals); optical clarity and transparency. It has been found that the efficacy of a nano-filled coating strongly depends on the effectiveness of the method used to uniformly disperse the nano-filler in the polymeric matrix. Furthermore, the presence of nano-particles should not impair the viscosity of the organic matrix, in order to employ the conventional techniques of application for coatings.