The removal of the lignin from the pre-hydrolysis liquor (PHL) of kraft-based dissolved pulp production is essential for the utilization of the saccharides in PHL. Horseradish peroxidase (HRP) was used to treat the PHL, and the treatment conditions for lignin removal were optimized, and the novel combined processes of HRP treatment and flocculation or acidification for lignin removal were proposed and evaluated. The results showed that the HRP treatment caused 33.3% dissolved lignin and 47.7% turbidity removal at the optimized conditions. The weight average molecular weight of the lignin in PHL increased from 1473 to 1719 g/mol with HRP treatment. The lignin polymerization catalyzed by horseradish peroxidase was of great benefit to the lignin removal in the subsequent processes. Compared to the processes of flocculation with poly diallyl dimethyl ammonium chloride (pDADMAC) or acidification, which caused 35.9% and 24.2% dissolved lignin removal, respectively, the combined process of HRP treatment and pDADMAC treatment or acidification at pH 1.5 caused more than 70% dissolved lignin and nearly completely colloidal lignin removal, accompanied by 12-13% saccharides loss.