Respiratory pathogens kill more people than any other infectious agent each year worldwide. Development of novel, economically friendly, sustainable, and highly efficient materials against viruses is a major challenge. Herein, we describe a nanostructured material composed of very small crystalline phosphate copper nanoparticles synthesized using a new biohybrid technology that employs a biological agent for its formation at room temperature in aqueous media. The evaluation of different enzymes in the final preparation of the nanomaterial or even in synthetic methods was performed. Biochemical characterization revealed the formation of Cu species in the protein network. The best biomaterial synthesized using a lipase called BioCuNPs showed excellent inhibition capacity against functional proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); for example, assent 3-chymotrypsin like protease (3CLpro) complete inhibition was achieved by using 5 µg/mL, or acetone (ACE)–spike protein interaction was inhibited by more than 80% in the presence of 400 µg/mL of BioCuNPs. Taking these in vitro results into account, an efficacy analysis against human coronavirus 229E (HCoV-E229) coronavirus was performed. A virus reduction of 99% was obtained in 5 min. Additionally, SARS-CoV-2 virus was tested to demonstrate high efficiency, with > 99% inhibition in 15 min using 500 microgram of material. To determine the wide applicability of this nanohybrid against viruses, an evaluation was carried out against a non-enveloped virus such as Human Rhinovirus (HRV-14), obtaining a virus reduction of 99.9% in 5 min. Finally, the virucidal capacity against different bacteriophages was also evaluated, obtaining an excellent inhibition effect against Phage ΦX174 (99.999% reduction in 5 min).