We have studied the synergistic activity of PGLa and MG2a, two antimicrobial peptides secreted by the African clawed frog, on phosphatidylethanolamine/phosphatidylglycerol mimics of the inner membrane of Gram negative bacteria using an array of experimental and theoretical techniques. In particular, we correlated the peptides’ dye-releasing capabilities from large unilamellar vesicles with the induced structural changes on the microscopic to nanoscopic length scales combining small-angle X-ray and neutron scattering with transmission electron microscopy and molecular dynamics simulations. At low concentrations and in the absence of pronounced dye leakage we found that MG2a is aligned parallel to the membrane surface in the lipid’s headgroup region and causes a relocation of PGLa from the backbone region toward the polar surface. In the synergistic regime, i.e. at high concentrations, the peptides transformed the unilamellar vesicles into collapsed multilamellar liposomes with the peptides acting as spacers between the bilayers. In this case, the PGLa and MG2a do not exhibit strong cross-interactions and show the tendency to form fiber-like structures. PGLa and MG2a synergism in phosphatidylethanolamine/phosphatidylglycerol mixtures consequently does not involve the formation of a stable peptide pore within the bilayer as conceived previously.