Abstract Background and objectives Maize ( Zea mays ) is a cereal of great commercial importance around the world. It has been reported that maize presents polyembryony (PE), which is described as the appearance of two or more seedlings from a germinated seed. Minerals and fatty acids (FA) play important roles in the growth and development of plants and animals. The objective of this work was to determine the minerals and FA content in embryo and endosperm of 32 maize genotypes kernels with different levels of PE (high [NAP], low [NBP], and nonpolyembryonic [T]). Findings The polyembryonic genotypes showed higher concentrations of calcium, magnesium, phosphorous, and potassium. In this study, magnesium was only found in the embryo, while in the embryo of NAP genotypes were found the highest content of K (1,834 mg/kg) and P (656 mg/kg). In contrast, the highest amount of Mg (216 mg/kg) was found in the embryo of NBP genotypes. On the other hand, the highest Ca (251 mg/kg) content was found in the endosperm of NAP genotypes. The highest oil content was observed in NBP‐9‐EM genotype grains with 50.2%, while the highest percentage of oleic (29.10%) and linoleic acid (63.21%) was found in kernels of the NAP‐6‐EM genotype. Conclusions The polyembryonic maize has high mineral content, and some of them have been associated with the human diet; in addition, in these genotypes, high oil content (with the presence of essential FA) was observed. Significance and novelty These results are important because polyembryonic maize kernel may be an alternative for adequate nutrient and essential oils intake. In addition, to the better agronomic characteristics offered by polyembryonic maize genotypes, which may imply a greater income for maize producers.