Ruminant-derived foods, predominantly milk and meat, are globally recognized as staples of a high-quality diet. Despite their widespread popularity, there is a notable deficiency in comprehensive standards addressing the nutritional values and safety of these products. This gap significantly limits both the supply of and demand for premium quality milk and meat. This review endeavors to highlight the benefits of utilizing metabolomics for the evaluation of quality and safety in milk and meat products from ruminants. It identifies critical metabolites, genetic signals, and metabolic pathways related to the synthesis of ruminant-derived milk and meat, proposing their potential as nutritional or regulatory targets and biomarkers. These biomarkers are instrumental in predicting and assessing the quality and safety of dairy and meat products, offering guidance for quality-based pricing and food safety inspections in the market. This review offers a critical overview of current metabolomics-based platforms and tools for interpreting the quality and safety of ruminant foods. The core metabolic biomarkers and biological biosynthetic processes of milk and meat enhance our understanding of the interplay between conventional food production from animals and new synthetic biological technologies.