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Bioleaching involves a chemical-microbial-driven dynamic process of oxidation and dissolution, as well as precipitation and formation of surface secondary phases that change the copper sulfide exposure/occlusion profiles. This dynamic process determines the kinetics of copper sulfides bioleaching. Former studies have shown the microbiological dynamics of the leaching solutions, and most mineralogical studies have been done with pure copper sulfide species under controlled conditions. In this work we aim to unravel the link between the microbiology and the mineralogy during the bioleaching of a mainly primary copper sulfide ore through the determination of the surface microbial and mineralogical variations in time applying process conditions. The results showed that the microbial dynamics in the leaching solutions is not representative of the bioleaching process since it differs significantly from the one established at the ore surface. Moreover, a major and fast alteration of the primary copper sulfide minerals chalcopyrite (CuFeS2) and bornite (Cu5FeS4) was observed, having as the major bioleaching intermediate the formation of covellite (CuS). When the ore was subjected to a mesophilic inoculation, the microbial dynamics was modified, significantly changing the mineralogical dynamics of these primary sulfides and enhancing the overall kinetics of copper recovery.