Residues of pesticides in food are influenced by processing such as fermentation. Reviewing the extensive literature showed that in most cases, this step leads to large reductions in original residue levels in the fermented food, with the formation of new pesticide by-products. The behavior of residues in fermentation can be rationalized in terms of the physical-chemical properties of the pesticide and the nature of the process. In addition, the presence of pesticides decrease the growth rate of fermentative microbiota (yeasts and bacterias), which provokes stuck and sluggish fermentations. These changes have in consequence repercussions on several aspects of food sensory quality (physical-chemical properties, polyphenolic content, and aromatic profile) of fermented food. The main aim of this review is to deal with all these topics to propose challenging needs in science-based quality management of pesticides residues in food.