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This study looked at three climate smart technologies (CSA) experimented by farmers in Malawi in terms of soil quality and maize yields and compared to CFS. The three technologies were conservation agriculture (CA), maize–pigeonpea (Maize-PP) intercrops and a local organic and inorganic soil amendment known as Mbeya fertilization (Mbeya-fert), from 2018 to 2019. Particulate organic matter, soil organic carbon (SOC), N, P, K, Ca and Mg all significantly improved while bulk densities were lowered under the three CSA systems compared to conventional farmer systems (CFS). CA and Mbeya-fert improved maize yields by 51 and 19%, respectively, compared to conventional farmer practices. They concluded that employing these CSA technologies could enable farmers to be more resilient, productive and adapt better to climate change shocks leading to improved food security and livelihoods.