After hydrothermal pretreatment and enzymatic hydrolysis of wheat straw, a slurry rich in lignin but with a high content of inorganic substances, especially silica, and residual carbohydrates is produced. This slurry was used to develop an ethanol organosolv separation method to produce silica-free lignin fractions. The addition of para toluene sulphonic acid (PTSA) and the use of two alternative long-chain alcohols, oleyl alcohol or nonylphenol, were tested. In every reaction, two lignin fractions were produced and their molecular size and elemental composition were characterized. The yield of each fraction and the change in MWD were studied as a function of temperature and solid to liquid ratio. At 100, 150, and 200°C and with the use of PTSA, high-purity lignin fractions were obtained. After lignin fractionation with nonylphenol, a liquid silica-free product with high lignin content was obtained in yields between 17 and 72%.