Bacterial antibiotic resistance increased drastically in the last decades becoming one of the most important threat for human health. The understanding of phenomenon promoting 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 an important selective factor, as bacteria can use similar defense mechanisms to resist against biocides and antibiotics, such as overexpression of multidrug efflux pumps. However, bacterial adaptation strategies to biocides and cross-resistance development remained unclear. In particular, very few studies have focused on biofilms, which nevertheless constitutes the main bacterial lifestyle in food processing environments and which can greatly influence bacterial tolerance and adaptive strategies against biocides. The aim of this study was to investigate how the biofilm lifestyle influences the selection of antibiotic-resistant clones when exposed to biocides. Biofilms of 10 E. coli isolated along the food chain were exposed during one month to biocides and their resistances to three different antibiotics (rifampicin, gentamicin, and ciprofloxacin) were quantified each week. Exposure to triamine (N-(3-Aminopropyl)-N-dodecylpropane-1,3-diamine) and benzalkonium chloride increased significantly the quantity of rifampicin-resistant clones collected when comparing to controls exposed to water. WGS of 155 clones revealed recurrent genetic targets associated with each biocide adaptation. Triamine selects for mutations in the lipopolysaccharide formation genes (especially genes involved in O-antigen biosynthesis) while benzalkonium chloride was associated with the ribose. Additional experiments are still under process to deeply understand collective biofilm adaptation to biocides and antimicrobial cross-resistance emergence in variants.