Although beneficial microorganisms contribute positively to the physicochemical and sensory profile of food, the presence of spoilage or pathogenic microorganisms in food might result in undesired effects, such as organoleptic changes, food waste, economic losses, and serious health concerns. On the other hand, the extensive use of antibiotics in primary production, among other factors, has contributed to the emergence of antibiotic-resistant bacteria that might exhibit cross-resistance to other unrelated antimicrobial agents, such as biocides commonly used in the food industry. In this sense, characterizing the microbiome (collection of microorganisms) and resistome (collection of antimicrobial resistant genes) of food and food-contact surfaces is crucial for designing and implementing preventive or corrective measures to control the presence and growth of microorganisms. Culture-dependent techniques have been traditionally employed to identify and quantify specific microbial groups throughout the food chain. However, their limitations and the more comprehensive insights offered by culture-independent approaches have contributed to their growing adoption in recent years. This chapter outlines the methodology for characterizing the microbiome and resistome of food and food-contact surfaces using whole metagenome sequencing (WMS).