Updated project metadata. DNA-protein crosslinks (DPCs) obstruct essential DNA transactions, posing a serious threat to genome stability and functionality. DPCs are proteolytically processed in a ubiquitin- and DNA replication-dependent manner by SPRTN or the proteasome but can also be resolved via targeted SUMOylation. However, the mechanistic basis of SUMO-mediated DPC resolution and its interplay with replication-coupled DPC repair pathways remain unknown. Here, we show that the SUMO-targeted ubiquitin ligase RNF4 defines a major pathway for ubiquitylation and proteasomal clearance of SUMOylated DPCs in a DNA replication-independent manner. In addition, we provide evidence that a subset of DPCs can be SUMOylated and processed via transcription, independently of RNF4. SUMO modification of DPCs is mediated by PIAS4 and neither stimulates nor inhibits their rapid DNA replication-dependent proteolysis. Instead, SUMOylation provides a critical salvage mechanism to remove DPCs formed or persisting after replication, as we demonstrate that DPCs on duplex DNA do not activate interphase DNA damage checkpoints. Consequently, in the absence of the SUMO-RNF4 pathway cells can enter mitosis with a high load of unresolved DPCs, leading to defective chromosome segregation and cell death. Collectively, these findings provide mechanistic insights into SUMO-driven pathways underlying replication-independent DPC resolution and highlight their critical importance in maintaining chromosome stability and cellular fitness.