As renewable electricity sources emerge, the conversion of electricity and CO2 to carbon-based fuels (e-fuels) arises as a complementary or competing option to biofuels. This work provides a systematic performance comparison of both bio- and e-fuel pathways to identify characteristic differences and optimal applications of both production types. We construct a reaction network that features biochemical and thermochemical conversion of lignocellulosic biomass, transesterification of waste vegetable oil, and e-based routes (E-routes) using renewable H-2. The network is optimized for economic and environmental criteria using two pathway screening tools, i.e., Reaction Network Flux Analysis and Process Network Flux Analysis. Furthermore, we apply a linear combination metric to analyze the advantages of bio-e-hybrid designs on a global fleet level. The results show that lignocellulosic-based fuels are relatively inexpensive but typically incur energy-intensive separations and high carbon losses. E-routes, on the contrary, result in only small carbon losses and global warming potentials as low as 5 g(CO2,eq.)/MJ(fuel). However, they come at high cost due to the use of expensive renewable H-2. When combinations are considered, biomass can be utilized by upgrading it with e-based H-2. In the case of bio-e-hybrid ethanol plants, co-fermentation of sugars and utilization of CO2 emitted during fermentation are identified as viable low-cost options for carbon loss reduction. These hybrid pathway designs outperform combinations of purely bio-based and purely e-based pathways at the fleet level.