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Skeletal muscle weakness is a major component of age-associated frailty, but the underlying mechanisms are not completely understood. Drosophila has emerged as a useful model for studying skeletal muscle aging. In this organism, previous lab-based selection established strains with increased longevity and reduced age-associated muscle functional decline compared to a parental strain. Here, we have applied a computational pipeline (JUMPptm) for retrieving information on 8 post-translational modifications (PTMs) from the skeletal muscle proteomes of 2 long-lived strains and the corresponding parental strain in young and old age. This pan-PTM analysis identified 2470 modified sites (acetylation, carboxylation, deamidation, dihydroxylation, mono-methylation, oxidation, phosphorylation, and ubiquitination) in several classes of proteins, including evolutionarily conserved muscle contractile proteins and metabolic enzymes. PTM consensus sequences further highlight the amino acids that are enriched adjacent to the modified site, thus providing insight into the flanking residues that influence distinct PTMs. Altogether, these analyses identify PTMs associated with muscle functional decline during aging and that may underlie the longevity and negligible functional senescence of lab-evolved Drosophila strains.