This study explores different mechanisms of antimicrobial action by designing hybrid nanomaterials that provide a new approach in the fight against resistant microbes. Here, we present a cheap copper-polyaniline (Cu-PANI) nanocomposite material with enhanced antimicrobial properties, prepared by simple in situ polymerization method, when polymer and metal nanoparticles are produced simultaneously. The copper nanoparticles (CuNPs) are uniformly dispersed in the polymer and have a narrow size distribution (dav = 6 nm). We found that CuNPs and PANI act synergistically against three strains, Escherichia coli, Staphylococcus aureus, and Candida albicans, and resulting nanocomposite exhibits higher antimicrobial activity than any component acting alone. Before using the colony counting method to quantify its time and concentration antimicrobial activity, different techniques (UV-visible spectroscopy, transmission electron microscopy, scanning electron microscope, field emission scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectrophotometry, and inductively coupled plasma optical emission spectrometry) were used to identify the optical, structural, and chemical aspects of the formed Cu-PANI nanocomposite. The antimicrobial activity of this nanocomposite shows that the microbial growth has been fully inhibited; moreover, some of the tested microbes were killed. Atomic force microscopy revealed dramatic changes in morphology of tested cells due to disruption of their cell wall integrity after incubation with Cu-PANI nanocomposite.