Hen egg white lysozyme is an enzyme (EC 3.2.1.17) which catalysing hydrolysis of the bacterial cell walls by cleaving the β-1,4-glycosidic bonds between N-acetylmuraminic acid and N-acetylglucosamine residues. It has been demonstrated to have antimicrobial activity against Gram-negative bacteria such as E. coli. In this study, the effect of native lysozyme, dry-heated lysozyme, dry-heated enriched with iso-aspartyle, iso-aspartyle lysozyme, native-like lysozyme and succinimide lysozyme on both the outer and inner membranes have been investigated, in vivo. Activities of native and dry-heated lysozyme induce different consequences on the bacterial membranes. Dry-heated lysozyme induces larger and/or more pores in the outer membrane and it disrupt the membrane potential more efficiently. It can be assumed that these stronger effects on the bacterial membranes are due to the modifications in the physico-chemical characteristics of dry-heated lysozyme compared to native lysozyme. However, dry-heated lysozyme is a mixture of three different isoforms: iso-aspartyle lysozyme, native-like lysozyme and succinimide lysozyme. Each of the dry-heated lysozyme isoforms affords a specific disturbance of either the outer or the inner membrane.