A novel technique is proposed to achieve higher cell yield in extremophile fermentation. Because the accumulation of toxic compounds is thought to be responsible for low biomass yields, a bioreactor has been designed based on a microfiltration hollow-fiber module located inside the traditional fermentation vessel. Using the cultivation of the thermoacidophilic archeon Sulfolobus solfataricus theta as a model, a biomass of 35gl(-1) dry weight was obtained which proved greater than that of 2gl(-1) obtained in batch fermentation. The bioreactor was characterized by running several fermentation experiments to check the high stability of the membrane module to sterilization cycles, high temperatures, and acidic pHs, even for prolonged periods of time. It was shown that the exhaust medium is unable to sustain growth for the presence of toxic compounds, and ultrafiltration and ion-exchange techniques were used in all the attempts to regenerate it. The results demonstrated the ability of the method to lower inhibitor concentrations and prolong the growth phase, thus achieving high cell density. Furthermore, they indicated that the toxic compounds are ionic species of less than 1kDa.