Coal is a major resource in Australia, both for power generation and as an export good, however its environmental impact is of significant concern. The structure of coal is inherently complex and contains many heteroatoms, which negatively affect the combustion efficiency and cause pollution. This study reveals that pretreatment of two types of Australian coal, a lignite coal and a thermal bituminous coal, with low cost choline amino acid based ionic liquids, markedly reduces the particle size and heteroatom content. This method is rapid (3 h) and proceeds at a low temperature of 70 °C. FTIR, NMR and TGA analysis revealed that pretreated coal has reduced aliphatic carbon, carbonyl groups and sulphur compared to untreated coal. Choline arginate was the best performing pretreatment agent for both types of coal. This is attributed to multiple hydrogen bond acceptor sites on the arginate anion, which facilitates strong interaction with the coal surface. These results open new pathways towards more energy efficient and cleaner coal, using low cost ionic liquids.