The mechanism underlying the ionophoric activity of CyPLOS (cyclic phosphate-linked oligosaccharide, 2), a carbohydrate-based synthetic ion transporter decorated with four tetraethylene glycol (TEG) chains, has been investigated by an integrated electron spin resonance (ESR) approach. The mode of interaction of the ionophore with lipid bilayers has been studied by quantitatively analyzing the perturbations in the ESR spectrum of an ad hoc synthesized spin-labeled CyPLOS analog (6), and, in parallel, in the spectra of spin-labeled lipids mixed with 2. The results point to a positioning of the cyclic saccharide backbone close to the lipid headgroups, largely exposed to the aqueous medium. The TEG chains, carrying a terminal benzyl group, are deeply inserted among the lipid acyl chains, showing good mobility and flexibility. As a consequence, the order of the acyl chain packing is significantly reduced, and water penetration in the bilayer is enhanced. The resulting asymmetric perturbation of the bilayer leads to its local destabilization, thus facilitating, through a non-specific mechanism, the ion transport through the membrane.