The formation of inhibitor precipitations is the biggest operation issue during heap bioleaching process that due to increasing concentration of produced cations and anions that during dissolution process is generated and is caused decreasing permeability in system and inactivation of ores surface. Due to oxidation iron and sulfur and dissolution of sulfide ores, the effluent from process typically has a considerable amount of ferric and sulfate ions that will be accumulated and the concentration will be raised to critical amounts by passing time. By circulation of these ions in heap, precipitates such as jarosite, sulfate calcium and elemental sulfur on the particle surface are formed that they may cuase reducing biooxidation rate and process efficiency. Furthermore, the objective of this research was controlling the amount of aqueous iron and sulfate with jarosite and gypsum and additionally determination optimized condition for removing the foregoing ions from solution of biodesulfurization of coal. In this way, the solution of biodesulfurization of coal by using moderate thermophilic and acidophilic oxidizing iron and sulfur microorganisms such as acidithiubacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxans and ferriphilum was used. Then formation of precipitation of jarosite and sulfate calcium for removing iron and sulfate ions has been carried out. Initially, biodesulfurization in Erlenmeyer flasks with 200 cc Norris culture medium, at 15% inoculum (v/v) and 15% density pulp (W/v) has performed. For microorganism adaptation with coal the flasks were agitated at 45 o C, 150rpm and pH=1/5-1/8. Afterward, for preparing main solution, the biodesulfurziration of high-sulfur coal from Tabas mine (contains 4/6% sulfur) in a 50-L stirred bioreactor with a rotational speed 180 rpm in a with industrial culture medium has done. After 60 days and by separating solid from liquid and analyzing, it was found that the concentration of ferric ions was 2900mg/L and sulfate ions was 12800mg/L. After solid-liquid separation, for precipitating Ammoniom jarosite, the solution of biodesulfurization of coal was used. For this purpose, parameters such as temperature, time, amount of seed and Ammonia to iron molar ratio was investigated by using a response-surface test design. Finally, it was found that in determinate optimized conditions by software at 95 o C, 2/5 hours, Ammonia to iron molar ratio 0/8 and 40g/L seeds, final elimination of iron ions 98.5% was achieved. By increasing temperature from 85 o C to 95 o C and time from 2 to 6 hours, the rate of removing of iron ions from 88% to 98% was increased. By conducting elimination of sulfate ions process by precipitation of sulfate calcium under different determinate conditions of temperature, time, amount of seeds and pH in test plant, it was found that according to offered optimized conditions by software contains 90 o C, 2 hours, pH=3 and 50g/L seed, final elimination of sulfate ions 71% was achieved. For instance, when pH was increased from 1/5 to 3 and temperature was increased from 60 o C to 90 o C, final removed sulfate ions was increasing sharply from 30% to 70%. Finally, during two process of precipitation Ammoniom jarosite and sulfate calcium, approximately 99% ferric ions and 87.2% sulfate ions was eliminated and sulfate concentration reduced from 12800 mg/L to 1640 mg/L.