Microorganisms are implicated in the irreversible degradation that usually occurs during the distribution and storage of food items. This action proceeds as biological and/or chemical reactions in foods, handling wares, and food processing facilities, and are also dependent on other several environmental factors. This review discusses the main mechanisms involved in the loss of food quality for most important food items, including the growth and associated metabolism of microorganisms resulting in the possible changes, formation of toxic compounds with adverse biological effects, and the subsequent counteractive effects of antibacterial elements used in food handling (with emphasis on copper). Meanwhile, as food spoilage poses a huge economic burden worldwide, evidence shows that the knowledge of spoilage mechanisms and food interactions with microorganisms is still limited, and in effect, perspectives and outlooks are presented as guides for the future design of wares for food handling applications.