Agriculture in Africa requires substantial investments, public and private, to increase agriculture productivity and achieve food security. Climate-smart agriculture options showing a win-win potential between food security and climate change adaptation on one side, and mitigation on the other side would enhance the capacity of the agriculture sector to sustainably support food security, incorporating the need for adaptation and the potential for mitigation into development strategies. The paper discusses a three-phase methodology to analyze the national agriculture investment plans with reference to climate change mitigation, through a combination of biological and economic modeling. Agriculture investments which can deliver food security and adaptation benefits are tested for their mitigation potential through a rapid screening methodology aimed at verifying the potential increase in Carbon sequestration and reduction in greenhouse gases (GHG) emissions. The mitigation benefits are estimated using the Ex-ante Carbon balance Tool (Ex-act) which can estimate the impact on GHG emissions and carbon sequestration of different land use and change scenarios. Last, Marginal abatement cost (MAC) curves are built in order to identify the least cost options. MAC curves show the order in which measures can be implemented and the relative cost of mitigation measures. Malawi case study is used as empirical application of the proposed methodology.