Cyanogenic glycosides (CNGs) act as feeding or oviposition deterrents and are toxic after enzymatic hydrolysis, thus negatively affecting herbivore performance. While most studies on CNGs focus on leaf herbivores, here we examined seeds from natural populations of Phaseolus lunatus in Mexico. The predominant CNGs, linamarin and lotaustralin, were quantified for each population by using ultra-high pressure liquid chromatography-mass spectrometry. We also examined whether there was a correlation between the concentration of CNGs and the performance of the Mexican bean beetle, Zabrotes subfasciatus, on seeds from each population. The concentrations of CNGs in the seeds were relatively high compared to the leaves and were significantly variable among populations. Surprisingly, this had little effect on the performance of the bruchid beetles. Zabrotes subfasciatus can tolerate high concentrations of CNGs, most likely because of the limited β-glucosidase activity in the seeds. Seed herbivory does not appear to liberate hydrogen cyanide due to the low water content in the seed. This study illustrates the importance of quantifying the natural variation and activity of toxic compounds in order to make relevant biological inferences about their role in defense against herbivores.