Plukenetia volubilis or Inca peanut is a promising plant with high economic value. Its seeds can be pressed for oil production or roasted and served as a snack, while the dried leaves can be used to make a kind of tea. Although the oil from the cold‐pressed seeds has been proven to be safe for human consumption, little information is known about the other parts of the plant regarding safety. Thus, the aim of this study was to investigate the naturally occurring phytotoxins, including saponins, total alkaloids, and lectins in fresh and roasted Inca peanut seeds and leaves. In addition, cytotoxicity on several normal cell types including human peripheral blood mononuclear cells, human embryonic kidney cells, human hepatic stellate cells, and mouse fibroblasts as well as in vivo mutagenic properties was studied. This study showed that fresh Inca peanut seeds and leaves contain saponins, alkaloids, and lectins. However, roasting enables the reduction in alkaloids, saponins, and possibly lectins, suggesting that these phytotoxins become unstable under heat. Furthermore, Inca peanut seeds and leaves, especially after roasting, are safe to a variety of normal cell lines and do not induce DNA mutations in Drosophila expressing high biotransformation system. In conclusion, the data in this study indicated that high and chronic consumption of fresh seeds and leaves should be avoided. Heat processing should be applied before the consumption of Inca peanut seeds and leaves in order to reduce phytotoxins and potential health risks.