Greenhouse gas emissions in the transport sector can significantly be reduced by replacing fossil based fuels with green alternatives. Various alternative fuel concepts have been developed differing in used sustainable feedstock, synthesis technology and final fuel characteristics. Whether these fuels can succeed in the market will depend on the fuel net production costs, the expected cost reduction potentials and the political intention to mitigate climate change. Results of previous studies for the techno-economic assessment of alternative fuels are difficult to compare due to significant differences in the applied methodology, level of detail and key assumptions in terms of economic factors and market prices. In this work, a standardized methodology for techno-economic analysis of fuel production processes is presented and exemplarily applied on sustainable fuels from Fischer-Tropsch (FT) synthesis. The methodology was adapted from a best practice approach from chemical industry and consists of three main steps: (A) literature survey on feasible production designs, (B) flowsheet simulation and (C) techno-economic assessment with the in-house software tool TEPET (Techno-Economic Process Evaluation Tool). It is shown that the standardized approach enables qualitative and quantitative statements regarding the technical and economic feasibility of fuel synthesis concepts including the identification of the appropriate fuel production concept due to predefined framework conditions. Results from the case study on green FT fuels reveal that Biomass-to-Liquid (BtL) concepts have lowest production costs at high electricity costs, whereas the Power-to-Liquid (PtL) and Power and Biomass-to-Liquid (PBtL) concepts are superior at low electricity prices. Fuel production costs in the range of 1.2 and 2.8 (sic)(2014)/1 were estimated. (C) 2016 Elsevier Ltd. All rights reserved.