The inappropriate use of antibiotics and the inadequate control of infections have led to the emergence of drug-resistant strains. In recent years, metallo-pharmaceutics and metallic nanoparticles have been proposed as potential alternative antimicrobials due to their broad-spectrum antimicrobial properties. Moreover, recent findings have shown that combinations of transition metal compounds can exhibit synergistic antimicrobial properties. Therefore, the synthesis and design of bimetallic nanoparticles is a field worth exploring to harness the interactions between groups of metals and organic complex structures found in different microbial targets, towards the development of more efficient combinatorial antimicrobials composed of synergistic metals. In this study, we present a green synthesis of Ag–Fe bimetallic nanoparticles using an aqueous extract from the leaves of Gardenia jasminoides. The characterization of the nanoparticles demonstrated that the synthesis methodology produces homogenously distributed core–shell Ag–Fe structures with spherical shapes and average diameter sizes of 13 nm (± 6.3 nm). The Ag–Fe bimetallic nanoparticles showed magnetic and antimicrobial properties; the latter were evaluated against six different, clinically relevant multi-drug-resistant microbial strains. The Ag–Fe bimetallic nanoparticles exhibited an antimicrobial (bactericidal) synergistic effect between the two metals composing the bimetallic nanoparticles compared to the effects of the mono-metallic nanoparticles against yeast and both Gram-positive and Gram-negative multidrug-resistant bacteria. Our results provide insight towards the design of bimetallic nanoparticles, synthesized through green chemistry methodologies, to develop synergistic combinatorial antimicrobials with possible applications in both industrial processes and the treatment of infections caused by clinically relevant drug-resistant strains.