The presence of hazardous chemical compounds in foods is a growing concern in almost every country. Although some toxins come from microbial contamination, a major part comes from residues of pesticides used for plant health and food preservation. Despite plans to decrease their use, the concentration of hazardous residues encountered in food is growing. The societal solution to this issue is to find alternatives to chemicals and replace the most hazardous by biodegradable, fewer toxic compounds. However, as this greener transition takes some time, any transitory solution to decrease the risks of contamination is welcome. Among them, the stimulation of microbial pesticide degradation in food in a similar way to bioremediation in the environment would be very positive. In this review, we present the problem of food contamination, focusing on organophosphates and organochlorines, and the various possibilities of microbial decontamination. We discuss the possible use of microbial biocatalysts as a biopreservation tool. We conclude that, although this process is very promising, it lacks research taking into account the various degradation products and the elaboration of screening procedures able to choose some rare, efficient biopreservation strains.