A systemic perspective on energy innovation is required to design effective portfolios of directed innovation activity. We contribute a standardised set of technology-specific indicators which describe processes throughout the energy technology innovation system, ranging from patents and publications to policy mixes, collaborative activity, and market share. Using these indicators, we then conceptualise and develop benchmark tests for three portfolio design criteria: balance, consistency, and alignment. Portfolio balance refers to the relative emphasis on specific technologies. Portfolio consistency refers to the relative emphasis on related innovation system processes. Portfolio alignment refers to the relative emphasis on innovation system processes for delivering targeted outcomes. We demonstrate the application of these benchmark tests using data for the EU's Strategic Energy Technology (SET) Plan which spans six technology fields. We find the SET Plan portfolio generally performs well particularly in areas over which portfolio managers have direct influence such as RD&D funding. However we also identify potential areas of imbalance, inconsistency, and misalignment which warrant further attention and potential redress by portfolio managers. Overall, we show how energy innovation portfolios can be analysed from a systemic perspective using a replicable, standardised set of measures of diverse innovation system processes.