Fluoride toxicity to microorganisms was a predominant factor contributing to the failure of a commercial scale bioleach heap. An integrated control strategy for fluoride complexation without jarosite generation by stepwise adding ferric ions was first proposed to enable the bioleaching of the chalcopyrite associated with fluoride-bearing gangue mineral by Acidithiobacillus ferrooxidans. Chemical speciation calculation revealed that with the presence of Fe3+, the concentration of the main lethal fluoride to microorganism, HF, decreased dramatically. The pure culture study showed that the detrimental effect of fluoride on microorganism was eliminated by increasing the molar ratio of Fe3+/F- to 3:1. Furthermore, chalcopyrite bioleaching experiment revealed the minimum Fe3+/F- molar ratio that enabled the bioleaching was 6:1. Stepwise addition was an effective way to promote a balanced system and avoid the formation of jarosite caused by the excessive Fe3+. Above all, the introduction of Fe3+ is a feasible method for reducing the fluoride toxicity during the bioleaching of chalcopyrite, shedding light on the industrial applications.