The aim of the present research was to encapsulate rutin with phosphatidylcholine (PC) to form PC-rutin complex known as phytosome to overcome the fortification difficulties such as low water solubility and bioavailability. Rutin loaded nanophytosome (RNP) was prepared in different molar ratios of rutin to PC. Colloidal properties of RNPs such as particle size, polydispersity index, encapsulation efficiency and stability, turbidity, and effects of thermal processes and pH on the physical stability of RNPs were assessed. Phytosome structure and chemical stability of rutin were investigated by FT-IR spectroscopy and HPLC/UV–Vis spectrophotometry, respectively. RNPs with the ruitn: PC molar ratios of 1:3 showed the most physical and chemical stability (during 30 days of storage) with fine particle sizes (<100 nm) and encapsulation efficiency of 99%. The turbidity and pH of food models/samples were remained unchanged at the fortification level. RNPs showed the ability of masking undesirable features of rutin resulting the potential applications in fortification of food products with water insoluble nutraceuticals.