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Smallholder agriculture accounts for almost 80% of food production in sub-Saharan Africa (SSA). Most of the food produced is consumed with little processing or value addition that can increase income and provide better livelihoods. However, the agricultural sector is negatively impacted by climate change, threatening the region’s food supply across the different nodes of the food value chain. Women play crucial roles in the region’s agrifood systems – from production to agribusiness – shouldering a disproportionately higher burden of climate change amidst limited access to critical resources. Yet, women receive little support, even with the development of regional trade policies on the continent. The focus on industrial agriculture in Africa contributes to unsustainable practices that exacerbate social inequalities and increase environmental degradation, further reducing productivity and increasing hunger. Agroecology offers a viable alternative that can mitigate these negative impacts by enhancing biodiversity, improving soil health, building resilience and food sovereignty, and reducing dependence on harmful chemical inputs. In addition, agroecology can also increase income for farmers through green businesses that reduce environmental footprints. Nonetheless, agroecological transitions are not gender-neutral, as they have a profound impact on various vulnerable groups in Africa, including women, young farmers, migrants, refugees and others. The present brief focuses on gender dynamics in agroecological transitions of African food systems in order to inform and guide practitioners in investing and designing interventions at local and national levels across diverse value chains in SSA. It highlights significant contributions of agroecological practices in food production and entrepreneurship across the region. We have detailed how agroecology has enhanced women’s empowerment by increasing economic opportunities, food security, biodiversity, and building resilience in West, East and Southern Africa. Notwithstanding successes, this issue brief identifies several gaps and areas where gender can be integrated into the agroecological transition. These are resource accessibility, financial inclusion, gaps in gender-responsive policies and support services, capacity-building, labour-saving technologies, and sustainability of agroecology-initiative funding models. Other areas limiting the integration of gender in agroecological transition are a lack of holistic approaches for incorporating local knowledge of women and marginalised groups, and the need for collaborations and partnerships that will create a supportive environment for agroecological transitions. Addressing these gaps promises to strengthen the contribution of agroecological transitions to gender equality in food systems within SSA. Philanthropy can play a critical role in promoting agroecological transitions by working with government and private-sector partners to complement funding for organisations promoting gender-sensitive agroecological innovations that build on traditional knowledge. Such initiatives can advocate for enabling environments through gender-sensitive policies and investments for agroecology-based startups.