To develop novel biorefinery concepts, the use of bio-based catalysts and solvents must be aligned with the principles of green chemistry. In this context, biogenic 2,5-furandicarboxylic acid (FDCA) is a very promising yet underused molecule with high potential for application as an acid catalyst, combining feasibility and sustainability with efficient and straightforward recovery. In this study, FDCA was evaluated as a catalyst in the recently developed OrganoCat pretreatment, a biphasic lignocellulose fractionation system. The catalyst was investigated for the efficient fractionation of the three main components-lignin, cellulose and noncellulosic sugars-with particular focus on the lignin quality, on the effect on enzymatic hydrolysis of the cellulosic residue, and on the noncellulosic sugar extraction. To address recovery of FDCA from the OrganoCat system, a method was developed, leading to the recovery of >97 % of FDCA with a spectroscopic purity of >99 %, maintaining full activity in consecutive runs.