Acetic and formic acid vapors emitted from woodwork in historical organs are very important corrosive agents for lead pipes. These acids are slowly released from the wood both during playing and when the pipes are silent. To inhibit this emission process, the wood surface can be modified, by creating a protective layer with alkaline features. However, a coating of wood is not recommended since this could modify the appearance and create a layer not perfectly compatible with the substrate. For this reason, we propose to use some innovative nanotechnology that has been successfully applied for the deacidification of wood samples coming from the Vasa shipwreck. Application of calcium (or magnesium) hydroxide nanoparticles, with sizes ranging from 30–150 nm, allowed a homogeneous distribution of particles through the surface layer of wood simply by soaking (or spraying) it in a alcoholic (or mixed with less polar solvents) dispersion of nanoparticles. Nanoparticles do not modify the wood appearance and distribute randomly within the first layers of wood. The small size of particles accounts for the high reactivity with CO2 from the air, to give the alkaline reserve of carbonates that provide high efficacy in the neutralization of gaseous acids. The emission of volatile organic compounds (VOC) from the treated wood was determined by using an emission test cell, Field and Laboratory Emission Cell (FLEC). The results show that the emissions of acetic acid vapor from nanoparticles treated wood was very low (< 70 μg/m2 h) during the first 13 month. In contrast, untreated wood emitted high concentrations of acetic acid vapor (200–400 μg/m2 h).