The invention relates to a method for the selective extraction of functionalised fatty acid esters from seeds of oleaginous plants, wherein said method includes: a) at least one step of extracting fatty acid esters that comprises simultaneously feeding into a reactor containing said seeds a light anhydrous alcohol, a basic catalyst and an extraction solvent non-miscible with said light alcohol and in which said functionalised fatty ester is not soluble in order to obtain a mixture of esters and glycerol; b) and at least one step of selectively extracting hydroxylated fatty acid esters by feeding into the reactor said extraction solvent in a backflush direction relative to the light alcohol in order to obtain an alcohol phase enriched with fatty acid esters, a glycerol phase and a cake. The invention can be used for obtaining a fraction having a high concentration of hydroxylated or epoxydised functionalised fatty acid esters, and a solvent phase containing the other non-functionalised fatty acid esters directly from the seeds of oleaginous plants.