Halloysite nanotube (HNT), a natural clay, was modified with branched polyethyleneimine (PEI) to form PEI-HNT using epichlorohydrin (ECH) as coupling agent, then protonated with HCl to obtain H-PEI-HNTs providing [NH3](+)[Cl](-) functionality for potential antimicrobial properties. Upon PEI modification, zeta potential value of HNTs was increased to +37.3 mV from -34.5 mV and to +41.1 mV for H-PEI-HNTs. Only 1.87 wt % H-element in HNT was increased to 3.03 wt % upon PEI modification along with newly generated elements of N and C at 2.99 and 9.93 wt %, respectively. Moreover, ionic liquid (IL) forms of HNTs with [NH3](+)[N(CN)(2)](-), [NH3](+)[PF6](-) and [NH3](+)[BF4](-) functionality were generated via anion exchange of H-PEI-HNTs with sodium dicyanamide (SDC), ammonium hexafluorophosphate (AHFP), and sodium tetrafluoroborate (STFB). The antimicrobial properties of the modified, protonated, and IL forms of HNTs were determined via macro dilution, diffusion and agar screening tests against Escherichia coli ATCC 8739, Pseudomonas aeruginosa ATCC 10145, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 6538 strains, and Candida albicans ATCC 10231 strains. It was found that H-PEI-HNTs possesses potent antimicrobial effect compared with the other forms of HNTs with 2-4 mg mL(-1) MIC and 8-16 mg mL(-1) MBC values via the macro dilution method. (c) 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 48352.