In southern Africa, most farming systems exhibit a close integration of crop and livestock components, with an output of one component being an input of the other. The allocation of crop residues for livestock feed meets two out of three critical objectives; it ensures feed during the dry season (De Leeuw, 1996), improves quantity and quality of manure to restore soil fertility (Murwira et al., 1995) but does not ensure permanent soil cover required under conservation agriculture (CA). Thus under CA, there are strong trade-offs for either allocating crop residues for livestock feed or using the crop residues directly for mulch thereby reducing the amount and quality of manure available and compromising the condition of livestock. The objective of this study is to perform a comparative analysis of maize grain yield and soil organic carbon (SOC) changes in CA systems versus conventional tillage systems with manure application. Crop residue retention and reduced tillage are options that are expected to increase SOC in the long-term, in a similar way to manure application. Therefore, it is necessary to perform a comparative analysis to quantify the differences and to identify the most sustainable system. Crop yield is important for ensuring food security and income, and SOC is an important determinant of soil fertility, productivity and sustainability (Lal, 1997).