The production of sustainable, biomass-based synthetic natural gas (SNG) and Fischer–Tropsch (FT) diesel can contribute significantly to climate neutrality. This work aims to determine the commercial-scale production costs and CO2 footprint of biomass-based SNG and FT diesel to find suitable integration scenarios for both products in the Austrian energy system. Based on the simulation results, either 65 MW SNG and 14.2 MW district heat, or 36.6 MW FT diesel, 17.6 MW FT naphtha, and 22.8 MW district heat can be produced from 100 MW biomass. The production costs with taxes for wood-based SNG are 70–91 EUR /MWh and for FT diesel they are 1.31–1.89 EUR /L, depending on whether pre-crisis or crisis times are considered, which are in the range of fossil market prices. The CO2 footprint of both products is 90% lower than that of their fossil counterparts. Finally, suitable integration scenarios for SNG and FT diesel in the Austrian energy system were determined. For SNG, use within the energy sector for covering electricity peak loads or use in the industry sector for providing high-temperature heat were identified as the most promising scenarios. In the case of FT diesel, its use in the heavy-duty traffic sector seems most suitable.