Acanthamoeba spp. are amphizoic protozoa capable of causing several severe diseases in humans and other animals, including granulomatous amoebic encephalitis and Acanthamoeba keratitis (AK). The high resistance of Acanthamoeba genus, especially in its cystic form, to most conventional disinfectants poses a challenge for its management through aseptic practices based on chemical disinfectants. The imidazolium salt (IS) (C16MImCl) demonstrated significant acanthamoebicidal potency against both trophozoites and cysts. However, its biocidal efficacy over a short exposure time, which will shed light on its potential use as a disinfectant, still needs to be studied. Therefore, the acanthamoebicidal effect of IS against trophozoites and cysts of Acanthamoeba polyphaga and Acanthamoeba spp. exposed for 5 and 20 min to concentrations of 250, 125, 62.5, 31.25, 15.62, and 7.81 μg/mL was evaluated in the present study. Exposure of trophozoites of both strains to IS for 20 min significantly reduced trophozoite viability at concentrations ≥62.5 μg/mL. All trophozoites of both strains were inactived 20 min after cessation of IS exposure at concentrations of ≥125 μg/mL for 5 min or ≥15 μg/mL for 20 min. Cyst viability of all strains was significantly reduced after 20 min of exposure to IS at 62.5 and 125 μg/mL, based on the viability exclusion assay with trypan blue dye. However, all cysts exposed to IS at ≥ 125 μg/mL for 20 or 5 min were unable to excyst when incubated for 10 days on non-nutrient agar with Escherichia coli. The acanthamoebicidal efficacy of IS, upon short exposure to concentrations below the cytotoxic value for human keratinocyte cells (IC50 = 171.50 μg/mL), combined with its previously reported bactericidal and fungicidal effects, suggests that IS has the potential to be used in the formulation of multipurpose disinfectants.