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Smallholder farming in southern African needs climate-smart agricultural approaches to adapt to current climate stress and climate variability, and increasing risk of these under future global climate change. There are a range of climate-smart systems that have been proposed and conservation agriculture (CA) based on minimum soil disturbance, crop residue retention and crop rotation is one of them. A CA trial established in 2007 in Malawi was used during cropping-seasons 2015-2016 (El Nino) and 2016-2017 (La Nina) to assess the performance and resistance of different CA maize systems under climate-related stress at anthesis, a climate sensitive growth stage. Large in-situ rainout shelters were used to simulate increased daytime temperatures and in-season droughts of 18-19 days and 27 days. CA systems better resisted climate stress around anthesis than conventional tillage practices as CA systems showed greater resistance to drought than conventional practice. This was expressed by higher CA maize grain yields, biomass yields or harvest index under conditions of natural (El Nino) or 19 day simulated drought. However, under 27 day drought simulation the resistance benefit of CA was no-longer significant. Crop diversification improved the resistance of CA systems to climate stress, more so when diversification was over time (rotation) than in space (intercropping). In all years CA systems substantially out yielded conventional practice, this highlights the benefits of medium-term (eight years) CA management before the rainout shelter experiment started. Our results from natural and simulated drought conditions confirm that CA systems can increase adaptive capacity to an increased risk of climate stress associated with projected global climate change. We show that large-scale rainout shelters are a useful means of accelerating our understanding of how long-term agricultural management practices can enhance resistance to climate stresses.