With economic development, the food industry and people's nutrition have experienced new growth. Food ingredients, as core elements of the diet, play an essential role in the food industry, but their microbial diversity and associated waste remain understudied. This study selected vegetables, fruits, seafood, meat, and their associated waste, commonly found at farmers' markets, for analysis using highthroughput techniques. It was found that Pseudomonas, Pantoea, Psychrobacter, and Acinetobacter were common bacteria in the samples. Meanwhile, methanogens and nitrogen-cycling archaea, such as Methanobrevibacter, Methanomicrobium, and Candidatus Nitrocosmicus, dominated the samples. However, the archaea showed no significant similarity between the samples. Further analysis revealed no significant differences between the microbial structures of fresh ingredients and their wastes, but more pronounced differences were observed between the microbial structures of fruits and vegetables and their respective wastes. Nitrogen-cycling archaea dominated fruit and vegetable wastes, whereas methanogens predominated in seafood and meat wastes. The co-fermentation process of fruit, vegetable, and meat wastes may facilitate C and N removal in the future.