Targeting the apical junctional complex during acute bacterial infections can be detrimental for the host in several aspects. First, the rupture of the epithelium or endothelium integrity is toxic in itself. In addition, extracellular bacterial pathogens or bacterial toxins can cross the body's physical barriers using the paracellular route and induce infection or intoxication of distant organs. No single strategy has been developed to disrupt junctional structures, rather each bacterium has its own method, which can be classed in one of the following three categories: (i) proteolysis/perturbation of adhesive proteins involved in tight or adherens junctions by bacterial or toxin-activated eukaryotic proteases, (ii) manipulation of host regulatory pathways leading to weakened intercellular adhesion, or (iii) delocalization of the junctional complex to open the gateway toward the subepithelial compartment. In this review, examples of each of these mechanisms are provided to illustrate how creative bacteria can be when seeking to disrupt cell-cell junctions.