Saponins are structurally diverse bioactive metabolites found in more than 100 plant families and are synthesized by plants as protection against insects, fungi, and other organisms. The mode of action is related to their interference with membranes, and particularly the membrane sterols. As membrane sterol composition varies across kingdoms and species, species-specific differences in toxicity may therefore be expected. The aim of this study was to elucidate the structure-activity relationships of different saponins across four different organisms (Daphnia magna, Enchytraeus crypticus, Saccharomyces cerevisiae, Raphidocelis subcapitata) representing three eukaryotic kingdoms of life using either immobility tests or growth inhibition assays. We hypothesized that monodesmosidic saponins are more bioactive due to higher amphiphilicity/polarity and that species susceptibility depends on sterol composition, with organisms containing plant sterols being less susceptible than those with animal or fungal sterols. The hypothesis was supported for monodesmosidic saponins, as α-hederin and hederacolchiside A1 exhibited significant cytotoxicity (EC50 values ranging from 8.7 to 36.9 and 2.0- 68.9 mg/L, respectively, for the different organisms), whereas bidesmosidic saponins such as hederacoside C and ginsenoside-Ro were inactive at concentrations up to 100 mg/L. The aglycone backbone and sugar moiety composition, however, also play critical roles, with simpler, linear saccharide chains leading to increased toxicity. C-23 hydroxylation has been shown to enhance mortality against insects; however, its absence did not affect the ability of hederacolchiside A1 to exhibit toxic properties. Additionally, species-specific sensitivities varied, with the crustacean D. magna being the most sensitive species, followed by the anelid worm E. crypticus, yeast S. cerevisiae, and the least-sensitive was, as hypothesized, the algae R. subcapitata. These insights contribute to a deeper understanding of saponin structure-activity relationships and open new avenues for the targeted development of saponin-based applications in agriculture, medicine, and biotechnology.