In this work, the use of silver-based silica nanocomposites (Ag@SiO2) was proposed to inhibit the microorganism growth of waterborne polyurethane adhesives. For that purpose, colloidal silver nanoparticles were prepared and embedded in a SiO2-based matrix in order to decrease the silver aggregation tendency. The protection of AgNPs with silica was also intended to improve the stability of the adhesive toward metallic particles. Last but not least, Ag@SiO2 provides safer handling of the silver nanoparticles due to their immobilisation within the silica matrix. Colloidal silver was prepared by the Creigthon method using NaBH4 as a reducing agent and polyvinylpyrrolidone (PVP) as a stabilising agent. The coating of the AgNPs by the silica matrix was achieved through a modified Stober process. The stability of the AgNPs in different amino-based catalysts for the silica matrix synthesis was evaluated in order to successfully obtain silver-silica core-shell nanocomposites. After that, AgNPs and Ag@SiO2 nanocomposites were incorporated in a waterborne polyurethane adhesive and the chemical, thermal adhesion and antimicrobial properties were evaluated.