Despite the fact that the topic of “women in research and innovation” has been on the agenda for decades and numerous measures have been implemented at both national and supranational levels to improve gender equality in research and innovation systems, it is still unclear which measures and under which conditions these measures are most effective. Even less research has been carried out on the effects of better representation of women in terms of research and innovation. This paper is based on the application of an innovative evaluation framework, which encompasses complexity and theory of change approaches and aims at exploring the link between interventions and their subsequent effects to two case studies. We discuss two major German flagship programmes aiming at increasing the participation of female researchers in the science system, the “Women Professorship Programme” and the “Pact for Research and Innovation”. Through the two programmes, we tested and validated the evaluation framework and its indicators. As part of the validation process, a theory of change has been developed for each of the programmes. The theory-based evaluation approach helped not only to identify gender equality impacts but also broader effects on research and innovation that might have otherwise remained undetected. We studied the effects of the two programmes on the number of women in leadership positions and analysed whether an increase in the proportion of women leaders influences publication patterns. Although linear linkages are challenging to establish due to the complexity of the process, the findings suggest that the flagship programmes have contributed not only to higher shares of women researchers but also to improved female publication and citation rates. There are clear benefits for Germany in terms of scientific results from the increased proportion of female researchers in research and innovation.