The Affordable Inputs Program (AIP) was introduced in Malawi as a flagship agricultural subsidy initiative aimed at increasing agricultural productivity, improving food security, and reducing poverty among smallholder farmers. Despite its broad coverage, concerns remain regarding the effectiveness and equity of its implementation. This study examines these concerns through the lived experiences and perceptions of smallholder farmers. Using qualitative secondary data, the study employs thematic analysis to explore three key areas: farmers’ perceptions of AIP’s impact on agricultural productivity and household food security, the equity of beneficiary targeting and selection processes, and experiences with program implementation. The findings indicate that while farmers recognize the value of subsidized inputs, the program’s effectiveness is undermined by significant implementation challenges. These include delays in input distribution, inconsistent input availability, weaknesses in beneficiary targeting and verification systems, inadequate rural and digital infrastructure and limited institutional capacity. Such challenges restrict timely access to inputs, reduce potential productivity gains, and weaken improvements in household food security. Furthermore, targeting and verification deficiencies contribute to inclusion and exclusion errors that undermine perceptions of fairness and program effectiveness. The study recommends strengthening rural and digital infrastructure, improving targeting and registration systems, enhancing distribution efficiency, and building institutional capacity to improve the overall effectiveness and equity of the AIP.