The virus inactivation efficacy of disinfectants is typically assessed by infectivity assay utilizing a single type of host cell. Enteroviruses infect multiple host cells via different entry routes, and each entry route may be impaired differently by a given disinfectant. However, it is poorly known how the choice of host cells affects the observed inactivation kinetics. Here, we evaluated the inactivation kinetics of echovirus 11 (E11) by free chlorine, ultraviolet (UV) irradiation, and heat, using three different host cells (BGMK, RD, and A549).