Elevated iron content in low-grade kaolin is one of the chemical factors detrimental for its industrial applications. Therefore, various physical and chemical methods have been applied to decrease iron concentration in kaolin. One of the more feasible and environmentally friendly method is biobenefication via microbially-induced bioextraction. Therefore, this paper provides data on fungal bioextraction of iron from kaolin sample when incubated with fungal Aspergillus niger strain. After 19-day cultivation, approximately 45% of iron impurities have been bioextracted by fungus and distributed into fungal biomass or culture medium. The bioextraction was triggered by both acidification of culture medium by fungus (below pH of 1.5) and organic acids production, which are biologically conversed from glucose. However, bioextraction of silicon and aluminium, which form building blocks of clay minerals in kaolin, was reasonably low and did not overcome 0.15%. Thus, our data indicate that the bioextraction of iron using A. niger strain for kaolin processing is a viable alternative method for increasing quality of the low-grade kaolin.