Iron and phosphorus deficiencies in alkaline soils threaten wheat by limiting nutrient availability due to their antagonistic relationship. This study tested if combining microbial incubation with foliar iron could synergistically improve wheat productivity and nutrition and mitigate deficiencies. A field experiment using a split plot design tested different iron and phosphate fertilization techniques. The main plots consisted of three iron application methods: foliar-applied iron (FL) at 2.5 kg ha−1, soil-applied iron (FS) at 5 kg ha−1, and no iron (F0). The subplots comprised four phosphate fertilizers: PSB + TSP (inoculation with phosphate-solubilizing bacteria + 100 kg ha−1 of triple superphosphate fertilizer), AMF + TSP (inoculation with arbuscular mycorrhizal fungi + triple superphosphate), TSP alone, and no phosphorus (P0). Foliar iron application with AMF + TSP increased seed potassium and root length density by 16.3-17.9% and 22.1-25.8% more than PSB + TSP, respectively. Under FS conditions, AMF + TSP exhibited 28.5-29.1% lower magnesium and 23.9-28.4% higher zinc seed concentrations compared to PSB + TSP, as well as higher levels of soluble proteins and lower concentrations of chlorophyll. There was no difference in grain yield between PSB + TSP and AMF + TSP for any of the iron treatments. Combining AMF + TSP and foliar iron application resulted in the highest grain yield, desirable seed nutrient content (particularly zinc, iron (>100 mg kg−1), and magnesium (>18 mg kg−1), improved root biomass, chlorophyll, and soluble proteins compared to PSB + TSP and TSP alone. This combination of microbial inoculation with foliar iron application is an effective strategy for mitigating the antagonism between iron and phosphorus and improving both crop productivity and nutrition.