An indirect bioleaching process for extracting at least one metal other than iron present in a material, said method comprising the steps of: a) supplying a ferrous ion in a first reaction space, b) oxidation of the supplied ferrous ion to ferric ion in a second reaction space, c) bioleaching of said at least one metal by said ferric ion in a third reaction space, characterised in that the step of supplying a ferrous ion is carried out, i) either by bioleaching of iron present in the material by a first bacterial population oxidising the iron and included in a first inclusion matrix and immersed in a first reaction medium present within the first reaction space, ii) or by acid leaching of iron present in the material by adding a strong acid, preferably sulphuric acid, in the first reaction space, iii) or by adding ferrous ions, in order to obtain a concentration of ferrous ions between 2 g/l and 50 g/l in the first reaction medium, and in that the steps of oxidation of the ferrous ion and bioleaching of said at least one metal are each carried out in a reaction space comprising a reaction medium and a bacterial population (B2, B3) comprising at least a population of iron-oxidising acidophilic bacteria, each of the bacterial populations (B2, B3) being included in a cell inclusion matrix immersed in each of the reaction media of each reaction space, the reaction media, the bacterial populations and the materials present in the different reaction spaces that can be transferred between these different reaction spaces, and in that an iterative oxidation of a ferrous ion, resulting from the bioleaching of said at least one metal to a ferric ion is carried out by the bacterial population present in the third reaction space, and in that the reaction spaces are different and the bacterial populations (B1, B2, B3) are not identical and in that a step of inclusion of a bacterial population in a cell inclusion matrix is integrated, which comprises the steps of: - Supplying a liquid inclusion medium, - Supplying a cell inclusion matrix compound in the inclusion medium in a weight to volume ratio between the inclusion matrix compound and the inclusion medium between 5 and 400 g/l. - Supplying an inoculum of the bacterial population in the inclusion medium, - Formation of a cell inclusion matrix comprising the bacterial population. a) supplying a ferrous ion in a first reaction space, b) oxidation of the supplied ferrous ion to ferric ion in a second reaction space, c) bioleaching of said at least one metal by said ferric ion in a third reaction space, i) either by bioleaching of iron present in the material by a first bacterial population oxidising the iron and included in a first inclusion matrix and immersed in a first reaction medium present within the first reaction space, ii) or by acid leaching of iron present in the material by adding a strong acid, preferably sulphuric acid, in the first reaction space, iii) or by adding ferrous ions, - Supplying a liquid inclusion medium, - Supplying a cell inclusion matrix compound in the inclusion medium in a weight to volume ratio between the inclusion matrix compound and the inclusion medium between 5 and 400 g/l. - Supplying an inoculum of the bacterial population in the inclusion medium, - Formation of a cell inclusion matrix comprising the bacterial population.