Genotype × environment interactions (G × E) induce differential response of soybean (Glycine max (L.) Merr.) genotypes to variable environmental conditions with respect to seed composition, and this may hinder breeding progress. The objectives of this study were to estimate the contribution of genotype, environment and G × E to seed chemical composition variability, and to identify the most stable non-transgenic genotypes for several chemical components. Seeds from six non-transgenic soybean genotypes that were grown in 23 environments in Argentina (24–38°S) were analysed. Although environment was the most important source affecting variation for most of the analysed chemical components, genotype and G × E also had a significant effect (P < 0.001). Stable genotypes with superior performance across a wide range of environments were ALIM3.20 for protein, linolenic acid (Len), Len : linoleic acid (LA) ratio (Len/LA), δ-tocopherol (δT) and total isoflavones (TI); ALIM4.13 for protein, oleic acid, α-tocopherol (αT) and δT; ALIM3.14 for Len, αT and TI; Ac0124-1 for Len and Len/LA; and Ac0730-3 for αT. Non-transgenic genotypes with stable chemical profile across environments would perform well under a wide range of environmental conditions for any chemical compound. This study contributes knowledge for breeders to use these genotypes to broaden the genetic backgrounds of currently available commercial cultivars, or to design production strategies that employ the genotypes directly as raw material.