This study investigated the genetic regulation of meat flavor differences in broiler chickens using metabolomics and transcriptomics. Protein phosphatase magnesium/manganese-dependent 1J (PPM1J) was identified as a key gene highly connected to meat flavor-related metabolites. Gain- and loss-of-function analyses revealed that PPM1J influences muscle atrophy, improves meat quality, and regulates glycerophospholipid composition by catalyzing protein dephosphorylation.