The invention relates to a process for decontaminating a biological material by partitioning and inactivation techniques. The process includes the formation of a three-layer liquid system (a-b-c), where the layers are placed one onto the other and are different from each other in density and/or miscibility properties. The upper layer (a) has an aqueous solution of the biological material to decontaminate; the lower layer (c) has the solution inactivating viruses, prions or bacteria; the intermediate layer (b), interposed between the upper and lower layers, separates and protects the biological material from the inactivating solution which has an organic solvent or a mixture of more such solvents, immiscible at least with the upper layer. Moreover, the invention provides specific indications about the density difference between the layers in order to preserve system stability and, at the same time, protect the efficiency of decontamination and the biological activity of the material undergoing decontamination.