The Farm Input Subsidy Program (FISP) in Malawi was introduced in 2005/06 season against the background of bad weather affecting production, prolonged food shortages and high input prices in the absence of soft farm input loans for smallholder farmers. The primary purpose of the program was to increase resource-poor smallholder farmers’ access to improved agricultural farm inputs to achieve food self-sufficiency and increased income through increased maize and legume production. This paper uses a recently released panel data of nationally representative sample households combined with geo-referenced climate and administrative data to analyze FISP targeting effectiveness and the program’s impact on a broad set of welfare outcome variables including consumption, caloric intake, marketed surplus and crop productivity, within a context of climate variability. Our study finds that Malawi’s FISP targeting needs to improve if the primary target is to reach resource-poor and climate-constrained households. Moreover, results show that the program is positively associated with household welfare, food security and productivity. Heterogeneity analysis also suggests that the program benefits households residing in areas characterized by higher climate variability, with a stronger impact for a larger level of treatment.