Agri-food by-products represent a considerable portion of the waste produced in the world and especially when incorrectly disposed of, contribute to air, soil, and water pollution. Recently, recycling of food waste has proven to be an attractive area of research for pharmaceutical companies, that use agri-food by-products (leaves, bark, roots, seeds, second-best vegetables) as alternative raw material for the extraction of bioactive compounds. Developers and producers are however, advised to assess the safety of nutraceuticals obtained from biowaste that, in virtue of its chemical complexity, could undermine the overall safety of the final products. Here, in compliance with EFSA regulations, we use the Ames test (OECD 471) and the micronucleus test (OECD 487) to assess the mutagenicity of two nutraceuticals obtained from food waste. The first consists of grape seeds (Vitis vinifera L.) that have undergone a process of food-grade depolymerization of proanthocyanidins to release more bioavailable flavan-3-ols. The second nutraceutical product consists of thinned nectarines (Prunus persica L. var nucipersica) containing abscisic acid and polyphenols. The results presented here show that these products are, before as well as after metabolization, non-mutagenic, up to the doses of 5 mg and 100 μg per plate for the Ames and micronucleus test, respectively, and can be thus considered genotoxically safe.