In this study, we propose a novel approach for the silica coating of silver nanoparticles based on surface modification with adenosine monophosphate (AMP). Upon AMP stabilization, the nanoparticles can be transferred into 2-propanol, promoting the growth of silica on the particle surfaces through the standard Stöber process. The obtained silica shells are uniform and homogeneous, and the method allows a high degree of control over shell thickness while minimizing the presence of uncoated NPs or the negligible presence of core-free silica NPs. In addition, AMP-functionalized AgNPs could be also coated with a mesoporous silica shell using cetyltrimethylammonium chloride (CTAC) as a template. Interestingly, the thickness of the mesoporous silica coating could be tightly adjusted by either the silica precursor concentration or by varying the CTAC concentration while keeping the silica precursor concentration constant. Finally, the influence of the silica coating on the antimicrobial effect of AgNPs was studied on Gram-negative bacteria (R. gelatinosus and E. coli) and under different bacterial growth conditions, shedding light on their potential applications in different biological environments.