Soybean (Glycine max L.) is an agronomic crop belonging to the legume family, and is the top second plant species with the highest iron (Fe) content. When exposed to Fe-deficiency during growth in the field, soybean yields are negatively affected from impaired chlorophyll biosynthesis, which is called as Fe-deficiency chlorosis (IDC). Although IDC in soybeans has been observed for years, the molecular studies to develop IDC-tolerant soybean cultivars were slower compared to the studies of other plant species. Recently, there are efforts to understand the molecular mechanisms behind IDC tolerance and use them to develop IDC-tolerant soybeans via molecular breeding and transgenic approaches. Genetic transformation of soybean is relatively easy, and loss-of-function mutant collections are readily available. There is a divergence in IDC tolerance among soybean cultivars, suggesting a potential improvement of soybean tolerance to IDC via molecular breeding. This mini review covers the latest developments in the field of soybean research to elucidate the molecular mechanisms of IDC tolerance. Soybean should be used a new model plant in understanding the Fe-deficiency tolerance mechanisms especially because of its high potential to be used as a bio-fortified crop to treat the iron deficiency in humans in the future.