Although bioleaching of chalcopyrite by thermophilic microorganisms enhances the rate of copper recovery, high temperature accelerates iron precipitation as jarosite, which can bring many operational problems in industrial processes. In this research, the bioleaching of chalcopyrite concentrate by the thermophilic Acidianus brierleyi was studied, and microbial growth, copper dissolution, iron oxidation, and jarosite precipitation were monitored in different initial pH (pHi). Bacterial growth was greatly affected by pHi. While bacterial growth delayed for 11 days with pHi of 0.8, this delay reduced to nearly one day for pHi of 1.2. Two stages of copper recovery were observed during all tests. High pHi caused fast bacterial growth in the first stage and severe jarosite precipitation in later days, causing a sharp decline in bacterial population and copper leaching rate. The copper recoveries after 11 days, were 25, 78, 84, 70, 56 and 39% for pHi of 0.8, 1.0, 1.2, 1.3, 1.5 and 1.7, respectively. Sulfur and jarosite were the main residues of bioleaching tests. It was revealed that the drastic effect of jarosite precipitation on microbial growth and copper recovery was mainly caused by ferric iron depletion from solution, rather than passivation of chalcopyrite surface. Slow precipitation of crystalline jarosite did not cause a passive chalcopyrite surface. The mechanisms of chalcopyrite bioleaching were discussed.