Melanoidins are brown polymeric material formed during thermal processing of food and widely distributed in the Western diet. Three water-soluble fractions were isolated from both commercial coffee and biscuit by sequential ultrafiltration steps (3 and 10 kDa cutoff). Biscuits were enzymatically digested to solubilize the protein-linked melanoidin fraction. Antimicrobial activity of melanoidins was evaluated against a Gram-negative reference pathogenic bacterium (Escherichia coli). The high-molecular-weight fraction of water-soluble melanoidins (>10 kDa) exerted the highest antimicrobial activity. The mechanism of action was further investigated by cell integrity and outer- and inner-membrane permeabilization assays. At the minimum inhibitory concentration, melanoidins provoked irreversible cell membrane disruption, which was independent of the bacterial transmembrane potential. Results indicate that water-soluble melanoidins killed pathogenic bacteria strains ( E. coli) by causing irreversible changes in both the inner and outer membranes. Likely, it allows for interference with biosynthetic processes, such as the inhibition of nutrient transport and macromolecular precursors.