In this study, first, the physicochemical cleaning of Cayirhan region's low-quality lignites was investigated by flotation to reduce ash content. In the flotation experiments, the effects of collector dosage, frother dosage, dispersant dosage, pulp density and air flow rate on ash content and combustible recovery in the concentrate fraction were optimized. Flotation tests were designed with Box Behnken design (BBD) which is a response surface method (RSM). The effective parameters and their interactions in lignite flotation are described with a mathematical model. After physicochemical cleaning, further desulfurization studies were carried out through biological treatment. Alternaria sp. Cf1 strain which was isolated from the same region lignites was used in microbial treatment for desulfurization studies. Sulfur emission values (EV) of studied sample, flotation and microbial treatment's concentrates were calculated and compared. After flotation and microbial treatments, sulfur emission values reduced from 12.76 to 1.01 to 0.34 for head sample, flotation and microbial treatment's concentrates, respectively that accounts for 97.37% total reduction in terms of dry ash free basis. (C) 2016 Elsevier Ltd. All rights reserved.