Purpose: Hydrophobic nutraceuticals are suffering from water solubility and physicochemical stabilities once administered to the body or food matrixes. The present study depicts the successful formulation of a zein-carboxymethyl cellulose (CMC) complex to stabilize a water in oil (W/O) emulsion to protect them from environmental and gastrointestinal conditions. The formulated water in oil in water (W/O/W) system was used for nanoencapsulating of hydrophobic nutraceutical, rutin, via protein-polysaccharide complexes. Methods: Zein nano particles smaller than 100 nm were produced using poly ethylene glycol (PEG 400) and Tween 80, which eliminates the use of ethanolic solutions in preparation of zein nanoparticles (ZN). CMC was then added to the ZN under magnetic stirrer to provide zein-CMC complex. A concentration of 20% CMC showed the smallest particle size (<100 nm). Rutin was dispersed in water in oil in water (W/O/W) emulsion stabilized by zein-CMC complex. A set of experiments such as encapsulation efficiency (EE%), encapsulation stability (ES%), and releasing rate of rutin were measured during 30 days of storage at 4°C. Results: Results showed that, produced multiple emulsion prepared with lower concentrations of Tween 80 (0.5%), ethanol: PEG: water ratio of 0:80:20 showed smaller size (89.8±4.2 nm). ES% at pH values of 1.2, 6.8, and 7.4 were 86.63±6.19, 91.54±3.89, and 97.13±2.39 respectively, indicating high pH tolerability of formulated W/O/W emulsions. Conclusion: These findings could pave a new approach in stabilizing W/O/W emulsions for encapsulating and controlling the release of water insoluble nutraceuticals/drugs.