This study assesses the impact of agricultural policy on soil fertility management and productivity in the smallholder maize-based farming system in Malawi. The study applies econometric and farm household modeling to address three specific objectives: to characterize factors affecting farmers’ choice and intensity of soil fertility management practices, to assess the productivity, profitability and technical efficiency implications of such practices, and to identify the most feasible options that maximize food security, i. e. household income, with lower soil fertility mining implications. The study recommends a soil fertility management policy based on complimentary strategies.