Oleoproteaginous and cereal seeds enclose a wide range of nutriments such as lipids, proteins, polysaccharides and various mineral and organic micronutrients. These nutrients are found under the form of natural assemblies such as oil or protein bodies or starch granules, that have interesting functionalities (micronic sizes, surface activity, high physicochemical stability, etc.). These assemblies are extracted by various processes using energy, organic solvents, steam, alone or in combination. Thus, their natural structures are often strongly damaged, and some of their functionalities disappear. Storming through natural assemblies’ biodiversity to address the societal demand for more natural and minimally-processed food, seems promising. Indeed, the soft extraction of such assemblies could be an alternative to traditional intensive fractionation methods of plant raw materials to isolate target ingredients (sucrose, starch, refined oils, etc.). This would allow energy savings and avoid solvent use, but must be balanced with potential challenges of this new green refinery scheme. The purpose of the present work is to highlight the physicochemical properties of various oil bodies from diverse plant origins. A green refinery protocol is proposed for their extraction from various matrices. Then their size distribution, surface activity, resistance to oxidation and fatty acids and liposoluble vitamins bioaccessibility is also presented. Omega-3 rich sources (linseed, chia, hemp…) are of special interest to correct the low dietary intake of US and European population as well as the ω6/ω3 balance. Oil bodies from these plant species can thus constitute new dietary carriers of ω3 and other bioactive molecules. Moreover, the combination of oil bodies with specific features (fatty acid profiles, stabilities, vitamin contents) can help meeting the requirements of specific nutritional targets (infants, children, elderly, athletes, etc.). Altogether, we are convinced that the valorization of these diverse oil bodies can be a strategic route in the development of sustainable food systems.