This review describes various food processing and addresses concerns related to food quality and safety using foodomics by mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Despite the operational practices adopted in the food sector, persistent issues that occur in response to the (non)biological factors and impact food quality and safety are reviewed. These issues involve chemical reactions, alteration, or loss of essential molecules, and the incidence of toxic substances in food. With the advent of foodomics, any adverse effects on the food molecular components (e.g., protein, lipid, metabolite) along the processing, production, storage, packaging, or further operations, are shown to be monitored. Subsequently, the proposed integrated approach can allow one to understand the degree of the quality and safety aspects of the food in relation with the efficiency of the processing, production, storage, or other treatments, in context. In suggestion, the approach holds promise and enables the food industry in producing high-quality foods with enhanced processing, preservation, and safety measures.