Conservation agriculture (CA) is increasingly promoted among smallholder farmers of sub-Saharan Africa in a quest to improve food security while sustaining the natural resource base of the agro-ecosystems where agriculture is based. The aim of this study was to investigate the effects of CA and traditional tillage on soil organic carbon (SOC) and selected hydraulic properties in two contrasting agro-ecological zones of Malawi. Six farmers hosted on-farm trials in each location, with each farmer having the following treatments: CA with continuous sole maize (CA-SM), CA with maize–legume intercrops (CA-ML), and traditional tillage with continuous sole maize (CT-SM). Soil samples were randomly collected in October 2015, from farmers’ fields located in Chipeni, Chinguluwe, Lemu, and Zidyana where CA had been implemented for 10 years (2005–2015) at six depth intervals: 0–10, 10–20, 20–40, 40–60, 60–80, and 80–100 cm. Bulk density, soil water characteristics, and pore size distribution were determined using undisturbed core samples. At all sites, CA improved total SOC, carbon stocks, and the stable fraction of particulate organic carbon. Maize–legume intercropping under CA had 35%, 33%, and 73% more total SOC than CT-SM in Chipeni, Lemu, and Zidyana respectively. In Chinguluwe and Lemu, CA-ML had 0.54 and 0.50 g kg–1 respectively more stable fraction of particulate organic carbon (POMP) than CT-SM; whereas in Chipeni, CA-SM had 0.73 g kg–1 higher POMP compared with CT-SM. CA also improved soil porosity, pore size distribution, and water retention capacity by increasing the proportion of mesopores and micropores compared with CT-SM. Thus, changing management practices from CT-SM to CA has the potential to improve the soil organic matter and soil hydraulic properties across agro-ecological zones in Malawi, which is important for sustainable agriculture. Farmers should be encouraged to minimise tillage, retain residues as mulch on the soil surface, and practice crop rotation.