Clean energy innovation is pivotal for low-cost energy sector decarbonization. Substantial public research and development funding is spent on energy innovation. Generating more evidence on which support mechanisms most effectively drive clean energy innovations, and why, could improve their design moving forward. In this Perspective, we discuss five challenges that researchers often face when attempting to rigorously evaluate energy innovation policies and public subsidy programmes. We recommend solutions, such as developing new innovation outcome metrics that consider unique features of the energy sector and building databases that cover long time periods. We also suggest that researchers and funding agencies work together to implement randomized control trials or conduct quasi-experimental evaluation of existing programmes and policies wherever possible.