Through integrative multi-omics profiling of human skeletal muscle, non-human primate skeletal muscle, and human skeletal muscle cell lines, we characterized the conserved protein accumulation and lysosomal remodeling signatures associated with skeletal muscle aging using proteomics, phosphoproteomics, and ubiquitinomics datasets. The human and primate tissue data were employed to define common aging phenotypes, while the cellular proteomic and phosphoproteomic data were further utilized to dissect the underlying molecular mechanisms. Together, this multi-omics dataset provides a systematic foundation for identifying key pathways and regulatory nodes in skeletal muscle aging.