This policy position paper is based on the discussions held during the Joint Conference on 22 October 2024, organized by the Horizon Europe gEneSys and NET4Air projects. The conference highlighted the importance of integrating gender equality and the gender dimension in the research and innovation (R&I) processes related to energy transition and advanced technological innovations (deep tech). Despite the distinct focuses of the two projects—gEneSys on social and gender inequalities in energy transition and NET4Air on air pollution monitoring using deep tech—common ground was found in their shared commitment to ensuring that public investment in innovation contributes to both technological progress and social sustainability. This paper outlines key recommendations for policy actions to address these challenges, foster innovation, and meet the European Union’s gender equality and sustainability goals.