The cytotoxic properties of two extracts from Chenopodium quinoa Willd. and three synthetic sapogenins were evaluated in different cancer cell lines (A549, SH-SY5Y, HepG2, and HeLa) to investigate their cytotoxic effects and determine if these cell lines activate the caspase pathway for apoptosis in response to saponin and sapogenin treatment. The saponin extracts were isolated from the agro-industrial waste of Chenopodium quinoa Willd., while the sapogenins were identified and quantitatively determined by High-Performance Liquid Chromatography (HPLC). Among these compounds, ursolic acid was the most active compound, with high IC50 values measured in all cell lines. In addition, hederagenin demonstrated higher caspase-3 activity than staurosporine in HeLa cells, suggesting an anti-cytotoxic activity via a caspase-dependent apoptosis pathway. HPLC analysis showed that the concentration of hederagenin was higher than that of oleanolic acid in ethanolic extracts of white and red quinoa. The ethanolic extracts of white and red quinoa did not show cytotoxic activity. On the other hand, the synthetic sapogenins such as ursolic acid, oleanolic acid, and hederagenin significantly decreased the viability of the four cell lines studied. Finally, by Caspase-3 assay, it was found that HeLa undergoes apoptosis during cell death because hederagenin produces a significant increase in PARP-1 hydrolysis in HeLa cells.