Large-scale deployment of both biochemical and thermochemical routes for advanced biofuels production is seen as a key climate change mitigation option. This study addresses techno-economic and environmental aspects of advanced liquid biofuels production alternatives via biomass gasification and Fischer–Tropsch synthesis integrated to a typical sugarcane distillery. The thermochemical route comprises the conversion of the residual lignocellulosic fraction of conventional sugarcane (bagasse and straw), together with eucalyptus and energy-cane as emerging lignocellulosic biomass options. This work promotes an integrated framework to simulate the mass and energy balances of process alternatives and incorporates techno-economic analyses and sustainability assessment methods based on a life-cycle perspective. Results show that integrated biorefineries provide greenhouse gas emission reduction between 85–95% compared to the fossil equivalent, higher than that expected from a typical sugarcane biorefinery. When considering avoided emissions by cultivated area, biorefinery scenarios processing energy-cane are favored, however at lower economic performance. Thermochemical processes may take advantage of the integration with the typical sugarcane mills and novel biofuels policies (e.g., RenovaBio) to mitigate some of the risks linked to the implementation of new biofuel technologies.