Yes in the crop of soybean the iron deficiency will lead to reduced yield and altered protein. The application of foliar iron chelates the acidification of alkaline soils and the use of resistant varieties are useful practices.
The protein metabolism is fueled by the photosynthesis engine has the iron deficiency affects this the yield and protein and oil contents can be affected. The fueling of the Rhizobium system is very much a function of being fed by the plant photosynthesis and micronutrients are needed more by the symbiotic bacteria than the plant directly. The application of micronutrient seed treatments in legumes can be very helpful for these micronutrient issues. Of course adapted Rhizobia strains with the micronutrients give better assurance of a productive result.
Iron affects many metabolic pathways and there are many classes of iron-containing enzymes. Therefore Iron will always affect protein content in a positive as well as negative way. Both have been observed in plant nutrition experiments. The result will depend on its interaction and relationship with other nutrients having much larger direct effect on protein content such as Nitrogen, Phosphorus and micronutrients such as Manganese and Zinc.
The first resort for iron chlorosis is the resistance of varieties. If symptoms are experienced the back stop would be iron chelate foliar sprays using Fe EDTA. I do think in legume crops the use of both micronutrient blend and seed inoculation is very important. In the case of trees the trunk injection treatments are possible. In trunk injection the chelate is injected into the vascular system using a pressure through a bore hole. The issues of iron chlorosis are largely related to alkaline pH and soil treatment such as sulfuring can eliminate chlorosis as the issue is not gross deficiency in the soil for immobility from carbonates pH and salinity.