The analysis of the reasons behind the persistent under-representation of women in senior positions in science is well-developed. In contrast, the assessment of the impact of policies addressing the problem suffers from a lack of evidence and an oversimplification of approaches. Based on the assessment of 125 programs for gender equality implemented in research organizations in Europe, North America, and Australia, we argue that holistic approaches and multidimensional frames of reference are needed for impact assessment, also to improve program design and policy. Our analysis shows that the problem of gender inequality is rooted in so many and interrelated factors that program impact assessment has to be multidimensional and complex. Having a conceptual approach grounded in the notion of complexity as a point of departure, the article presents an innovative impact assessment tool, pointing to effective ways to assess the impact of gender equality programs.