Woody biomass is an important renewable energy resource that can be used directly or indirectly in the electricity, heat and transport sectors. Different technologies and conversion pathways can be used to convert woody biomass to supply different types of energy services. The primary energy and climate implications of bioenergy systems depend on which conversion technologies and pathways are used to produce the energy services, as well as how the services would have been supplied without the bioenergy system. Here, we focus on bioenergy for transportation in the context of a total renewable-based energy system. We contrast two different pathways: (i) biomotor fuel production in stand-alone plants and (ii) bioelectricity production in standalone plants and district heating systems with CHP plants and heat storage capacity for electric and plug-in hybrid vehicles. We quantify the primary energy use and the instantaneous biogenic CO₂ of the two alternatives, per km of driving distance. We consider both commercially available technologies and emerging technologies for biomass-based conversion systems. Furthermore, for the two alternatives we discuss potential benefits of integration between the electricity, heating and transport sectors, to enable a better use of infrastructure. The results show that primary energy use and instantaneous biogenic CO₂ emission vary strongly between the alternatives. The primary energy efficiency is much higher and gives less instantaneous biogenic CO₂ emission for electric and plug-in hybrid vehicles compared to vehicles using biomotor fuels. Furthermore, the potential integration benefits between the electricity, heating and transport sectors are much larger due to the integration potential of heat storage capacity in DHS and battery storage capacity in electric and plug-in hybrid vehicles, as well as an improved overall integration capacity between the sectors. This study suggests that use of biomass should be considered in the context of the overall energy system, and in relation to the development of energy conversion technologies and integration potential between different energy sectors, to find primary energy efficient alternatives giving climate benefits in both a short- and long-term perspective.