Using gas-phase deposition (Physical Vapor Deposition (PVD) and Metal Organic Chemical Vapor Deposition (MOCVD)) methods, modern implant samples (Ti alloy and CFR-PEEK polymer, 30% carbon fiber) were functionalized with film heterostructures consisting of an iridium or gold sublayer, on the surface of which an antibacterial component (silver) was deposited: Ag/Ir(Au)/Ti(CFR-PEEK). The biocidal effect of the heterostructures was investigated, the effect of the surface relief of the carrier and the metal sublayer on antibacterial activity was established, and the dynamics of silver dissolution was evaluated. It has been shown that the activity of Ag/Ir heterostructures was due to high Ag+ release rates, which led to rapid (2–4 h) inhibition of P. aeruginosa growth. In the case of Ag/Au type heterostructures, the inhibition of the growth of P. aeruginosa and S. aureus occurred more slowly (from 6 h), and the antibacterial activity appeared to be due to the contribution of two agents (Ag+ and Au+ ions). It was found, according to the in vitro cytotoxicity study, that heterostructures did not exhibit toxic effects (cell viability > 95–98%). An in vivo biocompatibility assessment based on the results of a morphohistological study showed that after implantation for a period of 30 days, the samples were characterized by the presence of a thin fibrous capsule without volume thickening and signs of inflammation.