p62-positive cytoplasmic condensates form by liquid–liquid phase separation and act as hubs for protein quality control and stress adaptation. While they are recognized substrates of selective autophagy, the factors defining their composition and turnover remain unclear. We established a fluorescence-activated sorting strategy to purify intact p62 condensates for proteomic and ubiquitinome profiling. Using this approach, we previously identified vault particles as NBR1-dependent autophagic cargo, defining a new pathway termed “vault-phagy” (Dev Cell, 2023). Extending this platform, we now identify a ubiquitinated transmembrane protein as an additional condensate component. High-resolution imaging showed that vesicles carrying this protein accumulate within p62 assemblies, with a subset juxtaposed to nascent autophagosomes. Mutation of ubiquitination sites impaired vesicle incorporation and reduced p62 body clearance, demonstrating the requirement of ubiquitin modification in this process. These findings underscore the utility of purification-based approaches for dissecting condensate biology and reveal a mechanistic link between ubiquitinated vesicles and the autophagic turnover of p62 condensates.