The well-known antimicrobial effects of chitosan (CS) polymers make them a promising adjuvant in enhancing antibiotic effectiveness against human pathogens. However, molecular CS antimicrobial mechanisms remain unclear, despite the insights presented in the literature. Thus, the aim of the present study was to depict the molecular effects implicated in the interaction of low or medium molecular mass CS polymers and their nanoparticle-counterparts against Escherichia coli. The differential E. coli proteomes sensitized to either CS polymers or nanoparticles were investigated by nano liquid chromatography–mass spectrometry (micro-LC-MS/MS). A total of 127 proteins differentially expressed in CS-sensitized bacteria were predominantly involved in (i) structural functions associated to the stability of outer membrane, (ii) increment of protein biosynthesis due to high abundance of ribosomal proteins and (iii) activation of biosynthesis of amino acid and purine metabolism pathways. Antibacterial activity of CS polymers/nanoparticles seems to be triggered by the outer bacterial membrane disassembly, leading to increased protein biosynthesis by diverting the metabolic flux to amino acid and purine nucleotides supply. Understanding CS-antibacterial molecular effects can be valuable to optimize the use of CS-based nanomaterials in food decontamination, and may represent a breakthrough on CS nanocapsules-drug delivery devices for novel antibiotics, as the chitosan-disassembly of bacteria cell membranes can potentialize antibiotic effects.