This study presents the conceptual process design for the production of branched paraffins with high carbon number, based on the upgrading of alcohols synthesized from biomass-derived syngas and the economic evaluation and comparison with the Fischer–Tropsh (FT) process and biochemical pathways. Two routes, one based on n-butanol and another on isobutanol upgrading, are described and modeled in ASPENPlus™. The flow sheeting results reveal high performance for both process configurations, resulting in an aviation fuel yield 0.172 kg/kgfeedstock and a thermal efficiency of 40.5% in the case of employing a modified Methanol catalyst for the mixed alcohols synthesis (MAS). Such alternative pathways offer higher efficiencies compared to FT synthesis because specific products such as C12+ branched paraffins for jet fuel applications are achieved with higher selectivity in the conversion processes. The water balance at the whole process reveals that the annual demands for fresh water from a 190 MWth biorefinery plant are 641,000 m3, emerging the water management as an important issue with considerable environmental impacts. Simulations of the overall process show a rather high biomass carbon to product utilization ratio (up to 30%) leading to relative low CO2 emissions. The economic evaluation reveals that the Minimum Jet Fuel Selling Price in a FT plant (1.24 €/l jet fuel) is lower than the corresponding price in a MAS plant (1.49 €/l and 1.28 €/l for cases with different catalysts). The biochemical route based on Acetone–Butanol–Ethanol fermentation is considered as the most economically desirable option (0.82 €/l). Moreover, the option of selling organic compounds, which are produced intermediately (i.e. light and heavy olefins, C4 alcohol isomers) via the alcohols’ upgrading processes was proved promising enough for the feasibility of such biorefineries plants.