The World Health Organization (WHO) has determined a series of guidelines to contain the advance and spread of COVID-19 and other influenza viruses. Among them, frequent hand hygiene has been widely recommended, resulting in an increased consumption of alcohol-based antiseptic products or synthetic molecules. However, when used in excess, these products might cause adverse consequences for human health, such as dermatitis, and for the environment, i.e., the selection of resistant bacterial genotypes. One of the alternatives to overcome this problem is the replacement of common antiseptics by formulations based on natural bioactive compounds with antimicrobial/antiviral activity. In addition, by nanostructuring formulations, it is possible to increase the bioavailability, stability, solubility, and absorption of bioactives in biological systems. In this sense, this study aimed to develop an antiseptic nanoemulsion based on natural bioactive compounds with virucidal activity against SARS-CoV-2. For that, oil-in-water (O/W) nanoemulsions were prepared, being the oil phase composed by Melaleuca alternifolia essential oil, quercetin, PEG400, and surfactants, while the aqueous phase presented carrageenan and purified water. Physicochemical characterization and stability studies were developed to evaluate the viability of the formulations over time. In addition, bactericidal activities against Staphylococcus aureus and antiviral activity against SARS-CoV-2 were determined by in vitro assays. As a result, the average size of the nanoparticles was recorded at 150 nm, with a Polydispersity Index (PdI) of 0.2 and a zeta potential around −10.0 mV. The stability of nanoformulations indicated the occurrence of quercetin-dependent creaming and sedimentation. In addition, the products presented a minimum shelf-life of 3 months. Regarding the bactericidal activity, a minimum inhibition concentration of 1.25 % for S. aureus was found. The cytotoxicity and antiviral assays revealed that the nano-based products showed 100 % of viral replication inhibition and proved to be safe for epithelial cells. In conclusion, two antiseptic nanoformulations with high anti-SARS-CoV-2 activity and great industrial and pharmacological potential were developed.