Natural disasters, violent conflict and other adverse shocks severely disrupt food systems, causing or exacerbating food insecurity among many communities worldwide. This study examines the impact and mechanisms of an integrated home garden intervention on food security in South Sudan, a context severely affected by conflict, forced displacement, recurrent severe flooding, the COVID-19 pandemic and institutional fragility, where, at baseline, only 29% of households had adequate food consumption. Using a quasi-experimental design with three waves of panel data from 772 households over two years, we find that the intervention increased food security as measured through the Food Consumption Score by 33% after two years (4.4 points, 90% CI [2.8, 6.1], p < 0.01) while significant impacts were absent after one year. Improved nutritional knowledge, increased market-oriented production and, most notably, asset ownership explain 56% of this impact. Our findings demonstrate that home garden interventions are an effective policy tool to improve food access as well as broader resilience-building, supporting economic stabilization and livelihood recovery for highly vulnerable communities in crisis-affected contexts. Given their relatively low cost and high adaptability, home garden interventions merit consideration as a scalable response to persistent food insecurity in crisis settings.