Radiation shielding assessments may underestimate the expected dose if some isotopes at trace level are not considered in the isotopes inventory of the shielded radioactive materials. Indeed, information about traces is not often available. Nevertheless, the activation of some minor isotopic traces may significantly contribute to the dose build-up. This paper presents a new method (Isotopes Inventory Reconstruction—IIR) estimating the concentration of the minor isotopes in the irradiated material at the beginning of the cooling period. The method requires the solution of the inverse problem describing the irradiated material's decay. In a mixture of an irradiated uranium–plutonium oxide shielded by a set-up made of stainless-steel, porous polyethylene plaster and lead methyl methacrylate, the comparison between different methods proves that the IIR-method allows better assessment of the dose than other approximate methods.