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A covalently functionalized-multiwalled carbon nanotubes (f-MWCNTs) with 2-aminothiophenol (2ATP) supported cerium oxide nanoparticles (CeO2 NPs) adsorbed on selenium nanoparticles (Se NPs) (MWCNT(SH)/CeO2@Se NPs) was prepared using a simple chemical route and utilized for the inactivation of Gram-positive/negative bacteria and fungus. In this investigation, a mixture of cerium nitrate and selenium dioxide precursor salts in the presence of MWCNT(SH) in p-toluene sulfonic acid medium (0.5 M) was reduced with sodium hydroxide by hydrothermal method, and the pH was maintained at 4.5. The uniform dispersion and stability of CeO2@Se NPs are strongly influenced by the thiol group (–SH) present in MWCNT(SH) supporting matrix. Morphology and microstructure analysis revealed good dispersion of CeO2@Se NPs onto MWCNT(SH) support matrix. The FTIR and UV–Visible spectroscopy results clearly revealed that the CeO2@SeNPs were anchored on MWCNT(SH) matrix. The antimicrobial studies were performed against a set of microbes, and they showed that Gram-negative (G −) stains were relatively more susceptible to CeO2@Se NPs-loaded MWCNT(SH) than Gram-positive (G +) stains. MWCNT(SH)/CeO2@Se NPs exhibited comparatively better microbicidal activity than MWCNT(SH). This is due to the influence of thiol (–SH) groups in stabilizing and protecting CeO2@Se NPs on MWCNT(SH) support against their leaching and agglomeration processes and thus augments the microbicidal effect of MWCNT(SH)/CeO2@Se NPs. [ABSTRACT FROM AUTHOR]