In food industries, microbial contaminations are difficult to control due to the recurrent formation of biofilms that hinders antimicrobials penetration and efficiency. An understanding of Salmonella Enteritidis biofilms behavior under flow conditions is a key to develop efficient preventive and control strategies. S. Enteritidis biofilms displayed 5.96, 6.28 and 6.80 log CFU cm-2 under 0.006 cm s- 1, 0.045 cm s-1, and 0.087 cm s-1 flow velocities, respectively. Biofilms exposed to higher nutrient conditions under greater flow rates, induced significantly more biofilm biomass. To control biofilms, the disinfection efficiency of thymol (THY) was assessed under dynamic conditions by encapsulation it into two types of nanocapsules: monolayer (ML) nanocapsules prepared with a single carrier material (maltodextrin), and layer-by-layer (LBL) nanocapsules prepared by combining two carrier materials (maltodextrin and pectin). A combined mixture of ML and LBL nanocapsules at 1/2 their minimal inhibitory concentrations induced 99.99% eradication of biofilms developed under the highest flow conditions, after 5 h. ML nanocapsules decreased significantly bacterial counts during the first 0.5 h, while LBL nanocapsules eliminated the remaining bacterial cells and ensured a protection from bacterial contamination for up to 5 h by releasing THY in a sustained manner over time due to the thicker shell wall structure.