The cost of transport decarbonisation matters, yet little information is available. Policies need to reflect the costs to society. The European Union relies on the PRIMES model, a private model with limited transparency. Our research revealed its methodological deficiencies. Based on a revised PRIMES model, modelling was carried out and compared with an official impact assessment prepared for a key EU policy. Our modelling results indicate that crop-based bioethanol has negative abatement costs, biodiesel and biomethane have costs below 100 EUR/tCO2eq, electromobility falls in the range of 100–150 EUR/tCO2eq, cellulosic ethanol has costs above 200 EUR/tCO2eq, while advanced biodiesel has costs above 300 EUR/tCO2eq. Our results on carbon abatement costs suggest that policy-making has often been based on outdated modelling in the EU. With regard to transport decarbonisation policies, a large number of recent energy and climate proposals by the European Commission seem to have been misguided.