The main objective of the present study was to investigate mixtures of soy phosphatidylcholine (SPC) and glycerol dioleate (GDO) as encapsulation matrices for cranberry flavonoids. The effects of flavonoids loading into non-aqueous formulations, non-lamellar liquid crystalline phases, and their colloidal dispersions were studied by using synchrotron small angle X-ray diffraction, dynamic light scattering. Flavonoids incorporation is discussed with respect to the lipid aggregation behavior, self-assembled nanostructure, and chemical stability by using antioxidant activity assay. The obtained results show that SPC/GDO-based formulations can incorporate relatively high amounts of flavonoids and serve as liquid crystalline delivery vehicles in the form of bulk phases or colloidal dispersions. Practical applications: Our results show that SPC/GDO-based formulations can incorporate relatively high amounts of cranberry flavonoids. The effect flavonoid extracts on the nanostructure of bulk SPC/GDO LC phases are lipid weight ratio-dependent. Flavonoids loaded into SPC/GDO-based formulations and LC phases retain their antioxidant properties. The self-assembled lipid liquid crystalline systems protect bioactive compounds from degradation. These facts are important for the community working in the field of self-assembly of lipid structures, food chemistry, and delivery vehicles of nutraceuticals.