This paper analyses the impact of factors related to innovation and the environment, among others, on labour productivity in the Spanish transport sector. The methodological approach used in this study was based on the CDM structural model. The main advantage of this model is its capacity to integrate investment in R&D and the generation of knowledge and production innovation. The data used in the estimations were obtained from the Technological Innovation Panel (PITEC) database. PITEC is a panel-type database jointly prepared by the Spanish National Institute of Statistics (INE) and the Spanish Foundation for Science and Technology (FECYT). The econometric results show that reducing the environmental impact has a statistically significant and positive effect at all stages of the innovative process and above all on labour productivity of transport firms, where the improvement of labour productivity can reach 8.35% compared to non-ecoinnovative companies. This finding could alert firms in the transport sector to the need to improve their activities by adopting environmentally proactive attitudes.