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Social attributes such as gender, wealth, age, ethnicity, migration status and religion can confer systematic disadvantages by making it difficult for some groups and individuals to access public and private mechanisms of resource allocation or decision making. In this strategy, we set out possibilities for strengthening how we address gender concerns in the CGIAR Research Program on Forests, Trees and Agroforestry (CRP6). The strategy focuses on the management support processes and structures needed to improve the quality and volume of gender-responsive research in the CRP6, and is closely aligned with the CGIAR Consortium’s gender strategy. It synthesises gender-relevant research questions, outcomes and associated impact pathways that have been identified across CRP6’s five research components. It recognises, however, that gender-based disadvantages may not always be the most urgent in all settings and that substantial differentiation can exist among men and women and not only between them. Thus, while this strategy is clearly marked out as a gender strategy, our agenda is broader. We envision that a careful use of participatory methodologies, including in problem framing, provides good scope for locating the most salient features of disadvantage in each research setting and for ensuring their inclusion in the research and action process. Overall, this strategy views gender integration in research as a fundamental part of doing good science and approaches gender integration as a cross-cutting theme, which integrates gender analysis and research into each of the five components/research programmes of the CRP6.