Innovation systems provide an approach to understanding, and managing, the innovation process. The application of structural theory from the sectoral innovations systems literature and the functional theory from technological systems literature to a series of projects provides an opportunity to explore how weaknesses in the innovation system relate to innovation failure. Findings from fuzzy set qualitative comparative analysis of multiple cases indicate that the weaknesses of the innovation system are recurrent across cases, and therefore, amenable to policy or management intervention to improve innovation outcomes. The weaknesses in structural theory conditions are more consistent than the weaknesses in technological theory conditions.