Iron chlorosis in soybeans [Glycine max (L.) Merr.] is difficult to predict and can be reliant on several soil factors. The objectives of this study were to (1) determine the underlying factors conducive to iron chlorosis using exploratory factor analysis and (2) determine how individual soil variables impact iron chlorosis using a stepwise regression. This study evaluated seven locations in western Kansas, determining how the underlying soil factors influenced varietal performance, and with and without seed applied Fe fertilizer. Factor analysis was performed using the Varimax rotation and the Heywood convergence to get the best possible relationships. Factors were deemed significant if the Eigenvalues were greater than 1, and then removed if only one variable was present, making the factor trivial. Multiple regression analysis was performed using stepwise variable selection. Two significant underlying factors were related to iron chlorosis. Factor 1 was dubbed “Plant Chlorosis”, and soil NO₃-N and Electrical Conductivity contributed to high levels of plant greenness, and P and Ca had an antagonistic effect on plant greenness. Factor 2 was the soil iron availability factor, which was made up of soil DTPA-Fe and Mg levels that positively influenced soil available iron, and the Alkalinity Stress Index (ASI) (made up of pH and carbonates), which negatively impacted soil iron availability. These underlying factors occurred in all varieties and seed-applied Fe fertilizer treatments. These underlying factors were indicative of soil chlorophyll meter readings (CM) at the V3 and V6 growth stage, as well as in grain yield.