In this study, fractionation by sequential antisolvent precipitation was applied to ionoSolv lignins for the first time. Pretreatment with the aqueous low-cost protic ionic liquid N,N-dimethylbutylammonium hydrogen sulfate ([DMBA][HSO4], 80 wt % in water) was applied to Miscanthus (herbaceous), willow (hardwood), and pine (softwood) to extract lignin. Then, lignin was sequentially precipitated by the addition of water as an antisolvent. Fractionation appeared to be controlled by the molecular weight of lignin polymers. Fractions isolated with minimal water volumes were shown to have high molecular weight, polydispersity, thermal stability, and Tg (178 °C). Later precipitates were more monodisperse and had high phenolic and total hydroxyl content and lower thermal stability and Tg (136 °C). Addition of 1 g of water per gram of dry IL was able to precipitate up to 90 wt % of lignin. Fractional precipitation represents a novel lignin isolation technique that can be performed as part of the lignin recovery procedure enabling a high degree of control of lignin properties. The effect of the fractionation on lignin structural, chemical, and thermal properties was thoroughly examined by two-dimensional heteronuclear single quantum coherence nuclear magnetic resonance, gel permeation chromatography, thermogravimetric analysis, and differential scanning calorimetry and compared to the unfractionated lignin precipitate obtained by addition of an excess of water.