Microbial desalination cells (MDCs) are known among the bioelectrochemical systems for their green and cost-effective application in salt removal. However, the low efficiency of desalination compared to other chemical and membrane-based methods still holding this technology in laboratory and requiring further research and development (R&D) to establish actual plants. This study focused on integrating different applicable functions in one setup to promote applying MDCs in actual scale. In this research, the behavior of the MDC upon applying different salt concentrations in the desalination chamber was studied. Moreover, salt, sulphate and organic matter removal in acetate and sulphate-fed MDCs (A.MDC and S.MDC) were investigated. 10, 20 and 35 g/l of salt were successfully removed by using MDC technology. Sulphate removal of 72 was achieved within the S.MDC setup while similar current productions were observed in both A.MDC and S.MDC. Higher COD removal (88) was recorded in S.MDC compared to 65 in A.MDC. Furthermore, the microbial communities were characterized and Rubrivivax was identified as the dominant genus in A.MDC while Desulfobulbus, Geobacter and Desulfovibrio were the most abundant genera in S.MDC setup. © 2018 Elsevier B.V.