Abstract Background Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters. Results Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pHi; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 gCOD L−1 d−1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20–47 mS cm−1), while marine conditions resembled brine waters (>47 mS cm−1). Enrichments at optimal conditions of OLR 5 gCOD L-1 d-1 and pHi 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 gCOD L-1 d-1, which was later increased to OLR 10 gCOD L−1 d−1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm−1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities. Conclusions Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.