Paper that addresses the ongoing challenges in achieving effective gender equality in research and innovation, despite decades of targeted policies and interventions, highlighting the limited research on how increased female representation impacts research outcomes. Using an innovative evaluation framework grounded in complexity and theory of change, the paper investigates the effectiveness of gender-focused interventions in German research systems. Two major initiatives, the "Women Professorship Programme" and the "Pact for Research and Innovation," are evaluated to assess their impact on female participation and influence in the science system. Each programme’s theory of change was developed, enabling a thorough analysis of gender equality impacts and broader effects on research and innovation. Findings reveal that both programmes have contributed to an increase in female leadership in research, with observed benefits in publication and citation rates among women researchers. Although establishing direct cause-effect relationships is complex, the analysis suggests these flagship programmes have had positive, measurable impacts on female representation and scientific productivity in Germany. The study underscores the broader benefits of enhancing women’s participation in research and innovation, providing insights for improving gender equality in science globally.