Adoption of conservation agriculture (CA) is increasingly being promoted as a way of adapting agricultural systems to increasing climate variability, especially for areas such as southern Africa where rainfall is projected to decrease. The DSSAT crop simulation models can be a valuable tool in evaluating the effects of CA which are viable both economically and environmentally. Our objectives were: (1) to evaluate the ability of DSSAT to predict continuous maize (Zea mays L.) yield for conventional tillage (CT) and CA systems as well as maize yield for a CA maize-cowpea (Vigna unguiculata) rotation on an Oxic rhodustalf (2) to use DSSAT to project weather effect of climate change on yield, economic returns and risk in CT and CA systems. The DSSAT model was calibrated using data from 2007-2008 season and validated against independent data sets of yield of 2008-2009 to 2011-2012 seasons. Simulations of maize yields were conducted on projected future weather data from 2010 to 2030 that was generated by RegCM4 using the A1B scenario. The DSSAT model calibration and validation showed that it could be used for decision-making to choose specific CA practices especially for no-till and crop residue retention. Long term simulations showed that maize-cowpea rotation gave 451kgha-1 and 1.62kgmm-1 rain more maize grain yield and rain water productivity, respectively compared with CT. On the other hand, CT (3131-5023kgha-1) showed larger variation in yield than both CA systems (3863kgha-1 and 4905kgha-1). CT and CA systems gave 50% and 10% cumulative probability of obtaining yield below the minimum acceptable limit of 4000kgha-1 respectively suggesting that CA has lower probability of low yield than CT, thus could be preferred by risk-averse farmers in uncertain climatic conditions. Using similar reasoning, Mean-Gini Dominance analysis showed the dominancy of maize-cowpea rotation and indicated it as the most efficient management system. This study therefore suggests that CA, especially when all three principles are practiced by smallholders in the medium altitude of Lilongwe and similar areas, has the potential to adapt the maize based systems to climate change. Use of DSSAT simulation of the effects of CA was successful for no-till and crop residue retention, but poor for crop rotation. Refinement of crop rotation algorithm in DSSAT is recommended.