Biomolecular condensates are enriched in RNAs and RNA-binding proteins (RBPs), and this study presents a method, LLPS-CLIR-MS, to characterize protein-RNA interactions within these condensates. This method uses UV cross-linking and tandem mass spectrometry to identify specific interactions at the residue level. The study shows that sequence-specific RBP-RNA interactions are generally preserved in condensates, with some structural changes observed. The approach allows for the structural analysis of protein-RNA complexes in condensates, which is critical for understanding ribonucleoprotein (RNP) structures. The study also examines the role of RNA in condensates, showing that while RNA can suppress RBP phase separation, it also promotes nonspecific interactions that contribute to condensation. The findings suggest that sequence-specific interactions are maintained in condensates, and that additional unspecific contacts may form. The method was applied to various RBP-RNA complexes, including PTBP1 and FUS, revealing that specific protein-RNA contacts are preserved in condensates. In the case of SARS-CoV-2 nucleocapsid protein, the study found that while the protein binds specifically to RNA in the dispersed phase, the interaction becomes less specific in condensates, suggesting that unspecific interactions may play a role in phase separation. The study also highlights the importance of multivalent interactions in phase separation, with sequence-specific RNA-RBP interactions contributing to this process. The LLPS-CLIR-MS method provides a way to study protein-RNA interactions in condensates, offering insights into the structural changes that occur during phase separation. This method could be used to generate integrative structural models of RNPs in condensates. The study also discusses the limitations of the method, including the coverage of the protein-RNA binding interface and the need for similar amounts of cross-linked complexes in both phases. Overall, the study demonstrates that specific protein-RNA interactions are preserved in condensates, and that these interactions play a key role in phase separation.Biomolecular condensates are enriched in RNAs and RNA-binding proteins (RBPs), and this study presents a method, LLPS-CLIR-MS, to characterize protein-RNA interactions within these condensates. This method uses UV cross-linking and tandem mass spectrometry to identify specific interactions at the residue level. The study shows that sequence-specific RBP-RNA interactions are generally preserved in condensates, with some structural changes observed. The approach allows for the structural analysis of protein-RNA complexes in condensates, which is critical for understanding ribonucleoprotein (RNP) structures. The study also examines the role of RNA in condensates, showing that while RNA can suppress RBP phase separation, it also promotes nonspecific interactions that contribute to condensation. The findings suggest that sequence-specific interactions are maintained in condensates, and that additional unspecific contacts may form. The method was applied to various RBP-RNA complexes, including PTBP1 and FUS, revealing that specific protein-RNA contacts are preserved in condensates. In the case of SARS-CoV-2 nucleocapsid protein, the study found that while the protein binds specifically to RNA in the dispersed phase, the interaction becomes less specific in condensates, suggesting that unspecific interactions may play a role in phase separation. The study also highlights the importance of multivalent interactions in phase separation, with sequence-specific RNA-RBP interactions contributing to this process. The LLPS-CLIR-MS method provides a way to study protein-RNA interactions in condensates, offering insights into the structural changes that occur during phase separation. This method could be used to generate integrative structural models of RNPs in condensates. The study also discusses the limitations of the method, including the coverage of the protein-RNA binding interface and the need for similar amounts of cross-linked complexes in both phases. Overall, the study demonstrates that specific protein-RNA interactions are preserved in condensates, and that these interactions play a key role in phase separation.