The merits of three climate smart agriculture (CSA) technologies implemented by farmers were assessed in Machinga district of Malawi with respect to their soil quality and maize yield effects. Data were collected from farms implementing the three CSA technologies, namely 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. With respect to resilience and adaptation, 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. Higher annual biomass inputs and improved water infiltration from the Maize-PP intercrops were observed. With respect to productivity, CA and Mbeya-fert improved maize yields by 51 and 19%, respectively, compared to conventional farmer practices. With regard to climate change mitigation, increases in measured SOC in the top 20 cm depth compared to the conventional farmer practices amounted to 6.5, 12 and 10.5 t C ha −1 for CA, Mbeya-fert, and Maize-PP intercrops, respectively, over a period of 2-6 years. This suggests higher potential for carbon sequestration from CSA technologies. Furthermore, use of drought tolerant varieties, timely weeding and optimum plant populations, increased productivity. Improved gross margins from CSA practices were also apparent. Thus, 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.