Pomegranate, a subtropical fruit renowned for its sensory appeal and nutritional benefits, has garnered global attention due to its distinctive flavor profile and putative health benefits. Enhancing fruit quality, particularly in terms of flavor, could significantly boost consumer preference and market demand. However, the development of flavor is a complex process that requires a deep understanding of the metabolic pathways that contribute to it. In this study, a comprehensive metabolomics approach employing gas chromatography mass spectrometry (GC/MS) and liquid chromatography mass spectrometry (LC/MS) techniques was used to identify flavor compounds and their precursors. To account for distinctive pomegranate compounds, anthocyanins and punicalagins were analyzed as well. Four key flavor-related pathways (shikimate/phenylpropanoid pathway, terpenoid backbone biosynthesis, lipoxygenase pathway, and tricarboxylic acid cycle metabolism) were explored to identify the regulatory mechanisms behind flavor compound production. Notably, Wonderful, a dominant cultivar in California, up-regulated most pathways to produce flavor-related secondary metabolites from their precursors. These findings offer a valuable foundation for breeding efforts aimed at improving sensory traits in pomegranate, ultimately enhancing consumer satisfaction.