We report a new procedure, exploiting “green” chemistry, resulting in biocompatible magnetically-driven nanocomposites with high antibacterial and antifungal activities against ten tested bacterial strains and four Candida species. The nanocomposites consist of silver nanoparticles (NPs), biogenic magnetite NPs isolated from magnetotactic bacteria, and an environmentally friendly polymer – chitosan. These hybrids were prepared using an acidified chitosan suspension to cover biogenic magnetite NPs by a cross-linking method, followed by employing the NH₂ groups of chitosan for the reduction of silver salt in an alkaline medium. Thus, in the procedure, chitosan acts as (i) a biocompatible matrix surrounding the magnetite NPs, (ii) a reducing agent for the silver ions, and (iii) a linker between magnetic and silver NPs. The size of the resulting silver NPs and the total amount of silver involved in the nanocomposites can be simply controlled by the initial concentration of the silver salt used in the reaction mixture. The as-prepared nanocomposites reveal increased bactericidal and antifungal activity when compared to previously reported magnetic silver NPs systems which were not prepared by green synthetic routes. The use of biogenic magnetite with an uniform shape and size, the absence of any other reducing agent during synthesis, the simple control of silver NPs size and loading, the biocompatible character of chitosan matrix, and a high antimicrobial effect predetermine the developed nanocomposites for targeted applications in biomedicine.