The study examined the effect of agricultural input subsidy on nutrition in Malawi. The aim was to find out how Malawi’s Farm Input Subsidy Programme (FISP) affects nutrition. Household panel data from the Malawi Integrated Household Panel Surveys for the years 2010 and 2013 was used. To answer the research question, we estimated Poisson and Two-Stage Least Square (2SLS) regressions using instrumental variables. The results suggest a generally positive impact of the FISP on household nutritional status. A gender-disaggregated analysis indicates that while there was no difference in the direction of impact, the magnitude was higher for female-headed households relative to male-headed households. There was also evidence of a positive impact of food price fluctuations on nutritional outcomes. The findings emphasize the relevance of farm input subsidy programmes in reshaping agricultural and nutritional outcomes in developing countries.