Adequate intake of micronutrients is necessary to reduce widespread health issues linked to low intake of iron (Fe), zinc (Zn), boron (B), copper (Cu), and manganese (Mn). Because more than two billion people suffer from micronutrient deficiency globally, to address this problem, highly-nutritious ancestral Peruvian crops like tarwi can be an important component of food security. Thus, our work explores the tarwi micronutrient variability to select biofortified genotypes without affecting seed size and weight. Tarwi is a biofortified food because of its seeds' Fe, Zn, and B content. Furthermore, Boron showed a positive correlation between seed size and weight. At the same time, copper showed a negative correlation. Finally, six accessions (P14, P16, P21, T05, T08, and T25) that are biofortified for Fe, Zn, and B with excellent seed size and weight and with adequate levels of Cu and Mn; adding value to Peruvian biodiversity at a low cost is a starting point for a breeding program to prevent micronutrient disorders.