Recently, acidic ionic liquid water mixtures based on the hydrogen sulfate anion have been shown to effectively extract lignin from lignocellulosic biomass. This study analyses Miscanthus giganteus lignin isolated after extraction with the protic ionic liquid 1-butylimidazolium hydrogen sulfate ([HC4im][HSO4]) followed by precipitation with the antisolvent water. Several analytical techniques were employed, such as quantitative 13C-NMR, 1H–13C HSQC NMR, 31P-NMR, Py-GC-MS, GPC and elemental analysis. The analysis shows that the ionic liquid pretreatment breaks lignin-hemicellulose linkages and depolymerizes the lignin through the cleavage of glycosidic, ester and β-O-4 ether bonds. This is accompanied by solubilization of the newly generated lignin fragments. At longer pretreatment times, repolymerization of lignin fragments through condensation reactions occurs. The isolated lignins were carbohydrate-free, had low sulfur contents, low molecular weights. Early stage lignins were structurally similar to ball-milled lignin, while more treated lignins were enriched in p-hydroxyphenyl and guaiacyl units and had a high phenolic hydroxyl group content. We conclude that, depending on the treatment conditions, lignins with a variety of characteristics can be isolated using this type of ionic liquid solution.