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Limited research has focused on nanoparticle (NP) applications’ impact on edible wheat parts in a field environment. Here, we studied the nutritional quality of edible parts of wheat (<i>Triticum aestivum</i> L.) with a field experiment by spraying MnFe₂O₄ nanoparticles. Wheat was foliar sprayed with 0, 25, 50, and 100 mg/L composite manganese ferrite (MnFe₂O₄) NPs during 220 d of a growth period. Ionic controls were prepared using the conventional counterparts (MnSO₄·H₂O and FeSO₄·7H₂O) to compare with the 100 mg/L MnFe₂O₄ NPs. After three consecutive foliar applications, nanoparticles demonstrated a substantial elevation in grain yield and harvest index, exhibiting a noteworthy increase to 5.0 ± 0.12 t/ha and 0.46 ± 0.001 in the 100 mg/L NP dose, respectively, concomitant with a 14% enhancement in the grain number per spike. Fe, Mn, and Ca content in grain increased to 77 ± 2.7 mg/kg, 119 ± 2.8 mg/kg, and 0.32 ± 7.9 g/kg in the 100 mg/L NPs, respectively. Compared to the ion treatment, the 100 mg/L NP treatments notably boosts wheat grain crude protein content (from 13 ± 0.79% to 15 ± 0.58%) and effectively lowers PA/Fe levels (from 11 ± 0.7 to 9.3 ± 0.5), thereby improving Fe bioavailability. The VSM results exhibited a slight superparamagnetic behavior, whereas the grains and stems exhibited diamagnetic behavior. The results indicate that the nanomaterial did not accumulate in the grains, suggesting its suitability as an Fe and Mn-rich fertilizer in agriculture. Above all, the foliar application of nanocomposites increased the concentrations of Fe, Mn, and Ca in wheat grains, accompanied by a significant enhancement in grain yield. Therefore, the research results indicate that the foliar application of MnFe₂O₄ NPs can positively regulate wheat grains’ nutritional quality and yield.