Although an enormous amount of work has been done in the area of biohydrometallurgy, the influence of the inert solid matrix on metal extraction, and consequently the rate-controlling mechanism have not been fully understood. Actually, most studies have mainly focused on the bioextraction of metals from high-grade mineral concentrates. Such an approach is important in elucidating the diffusion and reaction phenomena that are taking place on the surface of the mineral. In reality, however, the mineral is embedded within an inert solid matrix which will have significant effects on diffusion and chemical reaction rate processes. In this work, a detailed experimental kinetic study was conducted to incorporate this factor in an attempt to quantify the rate-controlling mechanism involved. The biological dissolution of pyrite in the presence of acidophilic Thiobacillus ferrooxidans was investigated in a batch experiments on three distinct mine waste rocks. The experiments were conducted on two particle sizes and at three operating temperatures. Based on particle size and activation energies results, it was found that intraparticle mass transfer resistances were solely the rate-controlling mechanism for this process This new finding is different from that reported by other investigators who underestimated the importance of intraparticle mass transfer resistances. Also, because similar processes are ubiquitous in nature, this work should have broad applications.