ABSTRACT Background Amebiasis is an infectious disease caused by Entamoeba histolytica. It represents one of the three worldwide leading causes of death by parasites and a public health problem due to its frequency, morbidity, mortality, and easy dispersion. Objective The study was aimed to evaluate the in vitro effect of Lactobacillus spp. postbiotics on E. histolytica trophozoites (HM1-IMSS strain) and to determine morphometric changes in trophozoite membrane by atomic force microscopy (AFM). Methods Bioassays on trophozoites were conducted with lyophilized postbiotics at 0.1, 0.3, and 0.5 mg/mL concentrations, and trophozoite samples were obtained for AFM analysis Results Results indicated postbiotic inhibitory activity; the highest percentage inhibition was 89.63% at 0.5 mg/mL. Trophozoites nanomechanical analysis showed 28.32% increase in ruggedness and 56% decrease in size with treatments compared to the control. Conclusion Our study showed that the synergy of Lactobacillus postbiotics inhibited E. histolytica HM1-IMSS in vitro growth under axenic conditions, inducing morphometric alterations in trophozoites’ cell membrane. These results would allow designing strategies or treatments aimed at E. histolytica control in the future.