Metallic and nonmetallic nanoparticles are bioactive compounds that exhibit broad resistance to bacteria, fungi, and even viruses. In this paper, a deep eutectic solvent (DES) based on betaine, glucose, and ethylene glycol was used to obtain suspensions of silver, copper, and selenium nanoparticles. Depending on the nanoparticle precursor used, Ag, Cu, and Se nanoparticles (NPs) with an average particle size of 50–100 nm were prepared, and the properties of the products were confirmed by the STEM, XPS, DLS, and UV–VIS methods. The use of a DES, without the need for additional reactants, allowed the production of stable nanoparticles with increased bioactivity against microorganisms. The obtained systems showed high bioactivity against strains of S. aureus, E. coli, and C. albicans. Nanosuspensions, by generating reactive oxygen species (ROSs), caused enzyme inactivation and the inhibition of the metabolic processes of microorganisms. Particle-generated cell degradation processes were investigated through ROS generation assays, API assays, the determination of the MIC/MBC, and cell decomposition rate assays in the early logarithmic growth phase. Copper nanoparticles derived from copper(II) acetate were also highly active against the human influenza A/H1N1 viruses, human coronavirus (HCoV-OC43, Betacoronavirus 1), and vesicular stomatitis virus (VSV, Rhabdoviridae), showing a virus titer reduction of more than 93.7−99.96%.