Lipid liquid crystalline nanoparticles such as cubosomes and hexosomes have unique internal nanostructures that have shown great potential in drug and nutrient delivery applications. The triblock copolymer, Pluronic F127, is usually employed as a steric stabilizer in dispersions of lipid nanostructured particles. In this study, we investigated the formation, colloidal stability and internal nanostructure and morphology of glyceryl monooleate (GMO) and phytantriol (PHYT) cubosome dispersions on substituting β-casein with F127 in increasing proportion as the stabilizer. Internal structure and particle morphology were evaluated using small-angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (cryo-TEM), while protein secondary structure was studied using synchrotron radiation circular dichroism (SRCD). The GMO cubosome dispersion stabilized by β-casein alone displayed a V(2) (Pn3m) phase structure and a V(2) to H(2) phase transition at 60 °C. In comparison, F127-stabilized GMO dispersion had a V(2) (Im3m) phase structure and the H(2) phase only appeared at higher temperature, that is, 70 °C. In the case of PHYT dispersions, only the V(2) (Pn3m) phase structure was observed irrespective of the type and concentration of stabilizers. However, β-casein-stabilized PHYT dispersion displayed a V(2) to H(2) to L(2) transition behavior upon heating, whereas F127-stabilized PHYT dispersion displayed only a direct V(2) to L(2) transition. The protein secondary structure was not disturbed by interaction with GMO or PHYT cubosomes. The results demonstrate that β-casein provides steric stabilization to dispersions of lipid nanostructured particles and avoids the transition to Im3m structure in GMO cubosomes, but also favors the formation of the H(2) phase, which has implications in drug formulation and delivery applications.