The COVID-19 pandemic has clearly shown the importance of developing advanced protective equipment, and new antiviral fabrics for the protection and prevention of life-threatening viral diseases are needed. In this study, selenium nanoparticles (SeNPs) were combined with polyester fabrics using printing technique to obtain multifunctional properties, including combined antiviral and antibacterial activities as well as coloring. The properties of the printed polyester fabrics with SeNPs were estimated, including tensile strength and color fastness. Characterization of the SeNPs was carried out using TEM and SEM. The results of the analysis showed good uniformity and stability of the particles with sizes range from 40–60 nm and 40–80 nm for SeNPs 25 mM and 50 mM, respectively, as well as uniform coating of the SeNPs on the fabric. In addition, the SeNPs—printed polyester fabric exhibited high disinfection activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with an inhibition percentage of 87.5%. Moreover, a toxicity test of the resulting printed fabric revealed low cytotoxicity against the HFB4 cell line. In contrast, the treated fabric under study showed excellent killing potentiality against Gram-positive bacteria (Bacillus cereus) and Gram-negative bacteria (Pseudomonas aeruginosa, Salmonella typhi, and Escherichia coli). This multifunctional fabric has high potential for use in protective clothing applications by providing passive and active protection pathways.