Solarization has been commonly used method for last decades to eliminate weed and pathogen microorganisms which it is economic and environmental friendly. Despite of rising temperatures during soil solarization, some thermophilic or thermo-tolerant microorganisms may survive in the soil; therefore, natural soil flora re-establishes their activity soon after this practice. To evaluate the effects of different polyethylene cover materials as well as bio-fumigation applications, two years field experiments in 2011 and 2012 were carried out. In 2011, results revealed that heatsensitive microorganisms in the surface soil have been eliminated rapidly. Sub soil layer was not as heated as the surface, thus, the higher CO2 formation was determined in 15-30 cm soil depth. In the second year of experiment, heattolerant microorganisms become more dominant; therefore, the higher CO2 production observed in surface than the sub soil. According to the enumeration carried out in 2011, the highest number of fungi at 0-15 cm soil depth was determined on the plots covered by water filled bubbled sheet. In 2012, the highest value was determined in a soil samples taken from 15-30 cm deep of conventional solarization application. Bacteria number was reduced up to soil depth; however, the highest bacteria number observed in air bubbled cover sheet treatment. There were great fluctuation on actinomycetes numbers, thus it is hard to evaluate the best cover material considering the data gathered. It was determined that the effect of temperature increase by solarization application on soil microorganism activity varies significantly between the years.