Background: The understanding of phenomenon promoting antibiotic resistance selection and dissemination from farm to fork is crucial to limit the emergence of resistant bacteria. Massive use of biocides on food chain may constitute a contributing selective factor, due to similar defense mechanisms against biocides and antibiotics, such as overexpression of multidrug efflux pumps. However, bacterial adaptation strategies to biocides and cross-resistance development remain unclear. In particular, very few studies have focused on biofilms which can greatly influence bacterial tolerance and adaptive strategies against biocides. In this study we investigate how the biofilm lifestyle influences the selection of antibiotic-resistant clones when exposed to biocides. Methods: Biofilms of 10 E. coli isolated along the food chain were exposed during one month to 4 biocidal substances (benzalkonium chloride, polyhexamethylene biguanide, triamine and sodium hypochlorite) and their resistances to three different antibiotics were monitored. Resistant variants were then characterized through phenotypic and genomic analyses (WGS). Results: Exposure to triamine and benzalkonium chloride increased significantly the quantity of rifampicin-resistant clones collected when comparing to controls exposed to water. WGS of 150 clones revealed recurrent genetic targets associated with each biocide adaptation. Triamine selected for mutations in the lipopolysaccharide formation genes (especially genes involved in O-antigen biosynthesis) while benzalkonium chloride led to mutations in the ribose metabolism pathway. Conclusions: This work supports the effect of biocides on the bacterial evolution and the emergence of Antimicrobial resistance. Additional experiments are still under process to deeply understand collective biofilm adaptation to biocides and antimicrobial cross-resistance emergence in variants.