Building upon mainstream literature on concept and measures of innovation efficiency, this paper introduces a new method for the evaluation of R&D resources mobilisation in a Technological Innovation System framework. The method consists of the implementation of a quantitative set up for improving the representation and assessment of system dynamics, both internal (within the innovation system) and external (with respect to the economic system). An application to the case of the EU28 bioenergy technological system shows that almost 20% of the R&D potential was under-utilised in 2011-2012. Main determinants of this systemic failure were specific economic and policy factors, which conditioned allocation decisions. In particular, the preference bias induced by the general investment capacity of the system, openness to competition in the innovation challenge and the intensity of policy production. Conversely, innovation efficiency benefited from a relatively higher share of educated population and the evidence of an effective progress towards the achievement of specific policy targets positively impacted on an efficient utilisation of R&D resources.