The effect of phytantriol (PT)-based liquid-crystalline nanoparticles, cubosomes, on the lipid bilayer membranes has been investigated using the combined Langmuir-Blodgett/Langmuir-Schaefer (LB-LS) technique to form an h-1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) monolayer at the air-water interface and transfer the lipid bilayer onto the Au(111) substrate. Changes of the compression isotherms confirmed incorporation of cubosomes dispersed in the subphase into the h-DMPC monolayer at the air-water interface. The photon polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements of the gold electrode covered by the transferred DMPC bilayer showed for the first time how the incorporation of cubosome material affects the orientation and conformation of lipid molecules in the membrane. Exposure to cubosomes affected the packing of d(54)-DMPC bilayers and introduced disorder of chains by increasing the contribution of gauche conformation. The decrease of the tilt angle of the acyl chains of adsorbed DMPC in the whole range of potentials applied to the gold electrode confirmed that incorporation of cubosome material results in a more tightly packed bilayer. The presence of phytantriol molecules within the d(63)-DMPC matrix was confirmed by PM-IRRAS studies of the PT-related bands. The LB and PM-IRRAS studies demonstrated in a convincing way that PT-based cubosomes change the organization of model lipid layers leading to structural changes of the membranes which have to be taken into consideration when PT-cubosomes are employed as drug carriers.