The motivation for this study stems from two major concerns that are interlinked. First, the on-going food security crisis of African countries. Second, the negative impact greenhouse gas (GHGs) emissions from agriculture have on future food production which worsens the food insecurity problem. The conundrum SSA faces is the need to increase food output through productivity growth while minimizing GHG emissions. To measure changes in productivity growth and GHG emissions, this study evaluates agricultural performance of 18 African countries by utilizing the Malmquist-Luenberger index to incorporate good and bad outputs for the years 1980 to 2012. The empirical evidence demonstrates that productivity is overestimated when not considering bad outputs in the production model. The analysis will also provide a better understanding of the effectiveness of previous mitigation methods which would then allow for appropriate course of action to achieve the twin objectives of increasing agriculture productivity while reducing GHG emissions