Amoebiasis, a disease caused by the protozoan Entamoeba histolytica, represents a serious public health problem, mainly in developing countries. The first line of therapy for amoebiasis treatment is metronidazole (MTZ); however, clinical isolates of E. histolytica with resistance to MTZ and varying sensitivity to other antiamoebic drugs threaten the effectiveness of the prevention and treatment of this parasitic infection. Natural products stand out as a promising strategy to develop new, safe and more effective alternatives. In this study, we determined and compared the phytochemical profiles of Agave tequilana, Agave angustifolia, Agave rhodacantha, and Agave maximiliana and described their cytotoxic effect on E. histolytica trophozoites. The results show that the four Agaves kill E. histolytica in a species–time–dose-dependent manner. A morphologic analysis of the treated parasites showed evident morphological alterations suggestive of programmed cell death with nuclear alterations; it also highlighted the presence of rounded cells with protuberances/perforations in the membrane and cells that appeared to have exploded. The overall activity of Agave ethanolic extracts in E. histolytica can help provide new strategies to advance alternative treatments against amoebiasis.