Food insecurity and malnutrition are rising worldwide due to disruptions in food systems related to interconnected health-, climate- and conflict-related crises. Although governments globally are committed to addressing nutritional challenges, policy responses have increasingly focused on food security and, particularly, on food affordability. However, these short-term measures often overlook the necessity of integrating nutritious foods into the food system to ensure improved long-term nutrition. By drawing on the United Nations Committee on World Food Security's Voluntary guidelines on food systems and nutrition, this article outlines opportunities for policy-makers to integrate nutrition into key elements of the crisis response. Key policy areas where nutrition could be further integrated include social protection, agricultural investment, trade policy and urban planning. Strengthening the focus of nutrition in these measures will be essential to establish long-term incentives that support food systems transformation for improved nutrition. Drawing on theories of the policy process, I propose that stronger governance and cross-sectoral dialogue will be critical to achieve sustained nutritional outcomes. Health policy-makers can play a leadership role in supporting cross-sectoral policy change by carefully framing the policy issues, advocating for institutional structures that promote collaboration across sectors to prioritize nutrition, and strengthening the management of conflicts of interest in food system policy-making.