Some metal pollutants are corrosive in nature, are associated with fouling and slagging challenges of the coal boilers, are highly volatile and might cause air pollution and are catalyst poisoners during Fischer–Tropsch catalytic reaction. Therefore, this work describes an improved microwave-assisted sequential extraction (MW-ASE) method followed by ICP-OES/MS analysis for metal distribution determination in South African coal samples. The multivariate optimum conditions for each sequential step were 0.1 g, 200 °C and 5 min for sample amount, microwave temperature and extraction time, respectively. Under the optimum conditions, Ga, Sr and Ba were the only metals that showed solubility towards water, therefore, these metals are classified as highly mobile and eco-toxic under wet environmental conditions. Additionally, all the investigated metals showed solubility towards acidic conditions (HCl and HNO3). These results suggest that, most metal ions are predominantly bonded to sulphate, sulphide, and carbonate coal minerals. Alternatively, Ce, Cr and Y showed total extraction recoveries of ≤ 90%, confirming their strong affinity towards quartz coal minerals. In overall, the proposed MW-ASE method reported short extraction time (0.34 h), environmentally friendly reagents (H2O and diluted H2O2) and rapid multivariate optimization with acceptable extraction efficiencies (79–98%) and reproducibility (RSD ≤ 5%).