Kazakhstan–Siberian Network on Spring Wheat Improvement unites 18 spring wheat (Triticum aestivum L.) research and breeding programs and presents opportunities to study genotype × environment interactions. Trial data from six locations in Kazakhstan and Russia in 2017–18 were used for grain ionomics analysis to evaluate the relative contributions of environment and genotype to variation in elemental composition and to formulate a methodology to enhance concentrations of important minerals in grain. The effect of year was least important to variation. For several elements (P, S, Cu, Mn and Mo), the effect of site was 2–3 times higher than the effect of genotype. The effects of genotype and site were similar for Ca, Mg, Fe, Cd and Sr concentration. Average broad-sense heritability across six sites in both years was: (for macroelements) Mg 0.59 > Ca 0.50 > K 0.44 > P 0.30 > S 0.20; and (for microelements) Zn 0.44 > Mn 0.41 > Cu 0.40 > Fe 0.38. Biplot analysis grouped the traits into five clusters: (1) concentrations of Co, Cu, Mo and Sr; (2) concentrations of Mg, P and Zn; (3) concentrations of K and Ni; (4) protein content, concentrations of Cd, Fe, Mn and S; and (5) grain yield, concentrations of Ca and Rb. These associations reflect regional soil and environment variation independent of genotype. Protein content had positive and significant genotypic correlations with Mg (0.57), P (0.60), S (0.68), Fe (0.64), Cu (0.50), Mn (0.50) and Zn (0.53). A combination of high grain yield, relatively high protein content, and high concentrations of P, S, Mn, Cu and Zn (singly or combined) was identified in the genotypes Element-22 (check cultivar), Lutescens-3-04-21-11, and Silach. The study contributes to research and cultivar development to improve the nutritional profile of grain for consumers.