In the wake of the United Nations Food Systems Summit – the first of its kind – practitioners need to capture the abstract concept of the food system and learn how the process of transformation that they engage in contributes to food system outcomes or risk operating in silos. With that aim, we focus on sector analysis, interpreting changes in sector performance as food system outcomes. This makes food systems thinking more actionable. We share an application of the integrated framework in a particular case: rapid assessments of the impact of COVID-19 on the functioning of the horticulture, sesame, and seed sectors across seven low- and middle-income countries. We highlight lessons learned from applying the multi-level integrated framework for putting food systems thinking into practice.