A novel green protocol for the deacidifying consolidation of waterlogged archaeological woods through aqueous dispersions of polyethylene glycol (PEG) 1500 and halloysite nanotubes containing calcium hydroxide has been designed. First, we prepared functionalized halloysite nanotubes filled with Ca(OH)2 in their lumen. The controlled and sustained release of Ca(OH)2 from the halloysite lumen extended its neutralization action over time, allowing the development of a long-term deacidification of the wood samples. A preliminary thermomechanical characterization of clay/polymer nanocomposites allows us to determine the experimental conditions to maximize the consolidation efficiency of the wood samples. The penetration of the halloysite-Ca(OH)2/PEG composite within the wooden pores conferred the robustness of the archaeological woods based on the clay/polymer composition of the consolidant mixture. Compared to the archeological woods treated with pure PEG 1500, the addition of modified nanotubes in the consolidant induced a remarkable improvement in the mechanical performance in terms of flexural strength and rigidity. The pH measurements of the treated woods showed that the halloysite-Ca(OH)2 are effective alkaline fillers. Accordingly, the modified nanotubes provided a long-term protection for lignin present in the woods that are exposed to artificial aging under acidic atmosphere. The attained knowledge shows that an easy and green protocol for the long-term preservation of wooden artworks can be achieved by the combination of PEG polymers and alkaline tubular nanostructures obtained through the confinement of Ca(OH)2 within the halloysite cavity.