Biomass chemical conversion processes allow the production of solid, liquid and gaseous biofuels, which can substitute almost any kind of fossil fuel and the associated greenhouse gas emissions. Despite this potential, high investment costs and conversion losses reaching up to 30-40 % of the input biomass energy content are major barriers to a higher penetration of the chemical conversion processes. Thus, biomass is nowadays predominantly used for direct combustion. However, conversion losses of chemical processes may be compensated by the fact that biofuels can be used in more efficient technologies compared to standard raw biomass fuelled technologies. As an example, Synthetic Natural Gas (SNG) can be used in a cogeneration-heat pump system to produce heat, reaching an overall efficiency much higher compared to a wood boiler. In this work biomass conversion options are compared taking into account the complete energy conversion pathway, from the resource to the supply of energy services. The comparison is performed by evaluating the CO2 abatement potential of integrating these different pathways into a national energy system with a Mixed-Integer Linear Programming (MILP) modeling approach. The comparison is done with 56 scenarios, which are classified in two different groups. In the first group the choice of the biomass chemical conversion process is the only possible change in the system. In the second group, other changes are allowed in the energy system, such as an important deployment of efficient technologies. Results show that biofuels can allow for an overall better performance in terms of avoided CO2 emissions compared to direct combustion of biomass. To exploit this potential, however, it is necessary to link the production of biofuels to a wider deployment of the corresponding efficient end-use technologies.