Selenium sulphide is a well-known bioactive chemical, but its preparation in nanometric form stabilised in water has not been widely reported. In the article, extracts of cinnamon, curcumin, and pepper obtained using natural deep eutectic solvents (NDES) were used to obtain stable selenium sulphide nanoparticles. The analysis confirmed that selenium sulphide nanoparticles with an average crystallite size of 28–44 nm and a particle size of approximately 500 nm were successfully synthesised. The use of NDES stabilised the SeS2 nanoparticles and increased their bioactivity towards microorganisms. The obtained systems revealed high biocidal and antiviral activity against S. aureus, E. coli, P. aeruginosa, and C. albicans strains, Human influenza virus A/H1N1, and Betacoronavirus 1 (Human coronavirus HCoV-OC43). The SeS2 nanoparticles obtained in the NDES extract of curcuma strongly inhibited the growth of pathogenic fungi and bacteria with minimum biocidal concentration (MBC) values of 117.2, 117.2, 117.2, and 468.8 mg/dm3 against E. coli, P. aeruginosa, S. aureus, and C. albicans, respectively. The suspensions containing selenium sulphide nanoparticles stabilised by spice extracts were also highly active against influenza viruses and B-coronavirus, showing a reduction of over 99%.