Transitioning to biofuels is crucial for reducing greenhouse gas (GHG) emissions in transportation, but limited biomass availability requires maximizing carbon efficiency. This study evaluates Fischer-Tropsch liquid (FTL) production from biomass, focusing on the impact of partial electrification and carbon capture and storage (CCS) on efficiency and flexibility. Five configurations—ranging from a biomass-intensive base case to a fully electrified process—are simulated and assessed through techno-economic and GHG evaluations under fluctuating energy prices. Full electrification achieves the highest carbon efficiency, increasing carbon-to-liquid fuel conversion from 37 % to 91 %, but faces challenges due to high electricity demand (up to 2.5 MWh per MWh of fuel) and reliance on low-carbon grids. Partial electrification offers a cost-effective alternative, reducing production costs by up to 40 % compared to fully electrified cases, while maintaining a carbon efficiency of around 60 %. CCS enables net-negative emissions, though its viability hinges on sufficiently strong carbon pricing incentives. Compliance with sustainability mandates, such as Renewable Fuels of Non-Biological Origin (RFNBO) requirements, depends on access to decarbonized electricity. Overall, partially electrified BtL pathways enhance carbon utilization, reduce emissions, and offer resilience to market fluctuations. These pathways provide a promising balance of environmental and economic performance, outperforming both traditional BtL under high biomass prices and fully electrified e-fuels in terms of cost. Their advantages make them attractive from both investment and policy perspectives—especially in markets supported by stable electricity prices, carbon incentives, and sustainability-driven regulation.