Pathogens (disease-causing microorganisms) can survive up to a few days on surfaces and can propagate through surfaces in high percentages, and thus, these surfaces turn into a primary source of pathogen transmission. To prevent and mitigate pathogen transmission, antimicrobial surfaces seem to be a promising option that can be prepared by using resilient, mass-produced polymers with partly embedded antimicrobial nanoparticles (NPs) with controlled size. In the present study, a 6 nm thick Ag nanolayer was sputter deposited on polycarbonate (PC) substrate and then thermally annealed, in a first step at 120 °C (temperature below Tg) for two hours, for promoting NP diffusion and growth, and in a second step at 180 °C (temperature above Tg) for 22 h, for promoting thermal embedding of the NPs into the polymer surface. The variation in the height of NPs on the polymer surface with thermal annealing confirms the embedding of NPs. It was shown that the incorporation of silver nanoparticles (Ag NPs) had a great impact on the antibacterial capacity, as the Ag NP-embedded polymer surface presented an inhibition effect on the growth of Gram-positive and Gram-negative bacteria. The tested surface-engineering process of incorporating antimicrobial Ag NPs in a polymer surface is both cost-effective and highly scalable.