Biogenic amines and aminoacids are compounds commonly found in animal and plant foods and have high antioxidant power. Furthermore, they can be indicators of food security, especially in foods prone to anti-nutritional factors such as sweet potatoes. The purpose of this study was to evaluate the levels of biogenic amines and aminoacids by HPLC of colored sweet potato genotypes (purple pulp and orange pulp) after boiling, steaming, microwave, unprotected oven and protected oven (wrapped in aluminum). Changes in the amine and aminoacid profile were observed after heat treatment. There was a reduction of tryptophan and 5-hydroxytryptophan after cooking in most of the evaluated genotypes. In purple sweet potatoes, the tyramine content was lower in all genotypes after heat treatments. We observed that baking with protection and boiling increased dopamine and serotonin levels in 'JNRX12', 'Trabuca' and 'JNRX1'. Tryptamine and L-dopa levels were elevated in 'JNRX12', 'Trabuca' and 'JNRX2' after unprotected oven cooking. Microwave cooking increases spermidine levels in most purple samples, but also increases cadaverine levels. Cadaverine was not detected in the orange sweet potato samples. Cooking by microwave and steam increased the levels of serotonin, L-dopa and/or dopamine in orange genotypes and microwave processing is advantageous because it requires less time. Boiling, commonly used, did not interfere with the general levels of biogenic amines in orange pulp samples. In these genotypes, cooking in a conventional oven, with or without protection, induced an increase in the tyramine content. The consumption of colored pulp sweet potatoes after different thermal processing is beneficial to health and, in addition to ensuring digestibility and palatability, it promoted beneficial changes in the levels of biogenic amines and health-promoting aminoacids.