DNA-protein crosslinks (DPCs) are both endogenous and chemotherapy-induced genotoxic DNA lesions that, if not repaired, can lead to embryonic lethality, neurodegeneration, premature ageing, and cancer. DPCs are heavily polyubiquitinated, and the SPRTN protease and 26S proteasome have emerged as two central enzymes for DPC proteolysis. The proteasome recognises its substrates based on their ubiquitination status. However, how the SPRTN protease, an essential enzyme for DPC proteolysis, achieves specificity for DPCs is still not entirely clear. We found that the N-terminal SPRTN catalytic region (SprT) possesses a ubiquitin-binding domain that we named the Ubiquitin Interface of SprT Domain (USD). Using multiple biochemical, biophysical, and structural approaches, we reveal that USD binds to all homotypic and various branched ubiquitin chains in an avid manner. The increased growth of ubiquitin chains on substrates enhances SPRTN’s ability to bind to these substrates, which in turn boosts its proteolytic activity. To our knowledge, this is the first mammalian endopeptidase known to recognise and proteolyze substrates tagged with all tested ubiquitin chains - both homotypic and heterotypic - whose proteolytic activity increases with the length of the ubiquitin chains. SPRTN binding to ubiquitin chains via USD leads to approximately 67-fold higher activation of SPRTN proteolysis towards polyubiquitinated DPCs compared to unmodified DPCs. In contrast, the constitutive components of the replisome during unperturbed or translesional DNA synthesis, which are usually not heavily polyubiquitinated during DNA synthesis, are poorly degraded, if at all, by SPRTN. These findings demonstrate that the polyubiquitination of DPCs is the key signal for SPRTN’s rapid proteolysis and determines its substrate specificity for DPCs. We conclude that SPRTN is a universal DPC protease for all polyubiquitinated DPCs, regardless of the E3-ubiquitin ligase involved in DPC repair. We believe our work illustrates how the SPRTN protease specifically processes DPCs while minimising the cleavage of other replicative proteins.