Industrialised economies are currently confronted with the challenge of transitioning to a low-carbon energy system. Starting from the insight that ‘system innovation’ rather than incremental change is needed, we diagnose barriers and enablers for energy system transformation for the case of Flanders (Belgium). We thereby combine multiple perspectives: a techno-economic perspective to derive a technology-based vision on the energy transition, a technology innovation perspective to assess barriers and enablers regarding the upscaling of technological niche-innovations, and a system innovation perspective to address fundamental barriers and enablers associated with transformative system change. We highlight the complementary features of the three perspectives and describe how insights can feed into the development of energy transition pathways.