Biodiesel is an alternative to fossil fuels and it's known by its low stability. Natural antioxidants attract researcher interest as safe replacement of the toxic synthetic ones. The aim of this work is to evaluate the antioxidant activity of natural extracts from wheat industry by products (wheat germ and defatted wheat germ) using safe and eco-friendly solvents. Loading the more active aqueous extract in liposome nanocapsules to overcome on its solubility problem in lipid then using it to enhance the stability of biodiesel is the novelty of this work. The antioxidant activity of different extracts was measured by 2,2-diphenyl-1-picrylhydrazyl (DPPH•) and β-carotene-linoleic acid oxidation method (Coupled autoxidation). Total phenolic content and total flavonoid content were also determined for the different extracts. The oxidation and storage stability of biodiesel treated with defatted wheat germ aqueous extract loaded in liposome ,in comparison with control sample and biodiesel treated with synthetic antioxidant were evaluated using accelerated oven test. Water extracts of wheat germ and defatted wheat germ gave higher bioactive content and higher antioxidant activity than other solvents extracts. Moreover, biodiesel treated with liposome nanocapsules of aqueous extract gave higher stability than both control and samples treated with synthetic antioxidants. These results concluded that natural antioxidants from wheat industry by-products are a promising alternative to synthetic antioxidants and attract attention to more research about using liposome nanocapsulation in improving biodiesel stability.