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Nutrition is a fundamental aspect of human well-being, yet persistent deficiencies remain prevalent among vulnerable populations. In Madagascar, smallholder farmers experience chronic nutritional insecurity driven by limited dietary diversity and low resilience to shocks. These vulnerabilities were exacerbated by COVID-19-related disruptions to food access and fragile supply chains. Despite the presumed buffering role of home-based food production, its contribution to nutritional adequacy, and the temporal variability of nutritional supply during this period, remains insufficiently documented, with limited local evidence and few global parallels. This study analyzes primary data collected over six survey rounds from June 2019 to June 2021, covering 548 lowland rice-farming households in rural Madagascar. It has two objectives. First, it examines the changes in food consumption and nutrient supply before and after the COVID-19 outbreak period. We assess and compare food consumption patterns by food group and nutrient supply per adult male equivalent (AME) using the Wilcoxon matched-paired signed-rank test. Second, we investigate the impact of home-based food production, which is represented by the energy-based food self-sufficiency ratio (FSSR), on the nutrient supply, using a fixed effects regression model. The results indicated a dietary shift toward increased vegetable consumption and a reduced intake of animal-sourced foods after the COVID-19 outbreak. It caused an increased supply of vitamin A and calcium and decreased supply of vitamin B12, which is primarily derived from animal-sourced foods. Regarding the impact of home-based food production, the results suggest that approximately half of the study population’s energy requirements are met through home-based food production, with significant seasonal fluctuations. Fixed effects regression analysis demonstrated that the FSSR had a significant positive effect on energy and nutrient supply per AME, except for vitamin B12, and that this effect diminished after the shock. These findings highlight the importance of strengthening and intensifying home-based food production as a key strategy for nutritional improvement. However, additional factors such as increased income, which is related to animal-sourced food consumption, should be considered to address deficiencies, particularly vitamin B12 supply.