Agglomeration is commonly used for processing clay-rich ores in order to prevent undesirable effects, especially the risks of plugging or preferential channelling within the heap leaching piles. As the mechanical and chemical stability of the agglomerates is of crucial importance for the behaviour of the pile, a detailed characterization of the structure and porosity of agglomerates seems necessary. In the present study, uranium-bearing clay rich ore was agglomerated and agglomerates were studied before as well as after 10 days of leaching. A multi-analytical approach (by X-ray tomography, SEM, XRD and MIP analyses) was used for the study of the mineralogy, porosity distribution and textures of the agglomerates. X-ray tomography and SEM images showed that agglomerates were the result of coalescence and layering of micro-agglomerates where each one in turn was composed of a nucleus embedded within phyllosilicates and an aluminous silicate matrix. MIP analyses highlighted that unleached agglomerates had a low connected porosity (between 3 and 7%). During the 24 first hours of process, the connected porosity increased by a factor 2 because of the leaching of the aluminous silicate matrix and about 60% of the uranium was recovered. During the next 9 days, the formation of a secondary aluminous silicate matrix derived from the dissolution of illites resulted in the plugging of mesopores and therefore led to a decrease of porosity and uranium extraction extent.