Two of the biggest problems facing humankind are feeding an exponentially growing human population and preventing the accumulation of atmospheric greenhouse gases and its climate change consequences. Refined agricultural practices could address both of these problems. The research addressed here is an exploration of the efficacy of alternative agricultural practices in sequestering carbon (C). The study was conducted in Zimbabwe with the intent to (a) demonstrate the utility of micrometeorological methods for measuring carbon dioxide (CO2) exchange between the surface and the atmosphere in the short-term, and (b) to quantify differences in such exchange rates for a variety of agricultural practices. Four Bowen ratio energy balance (BREB) systems were established on the following agricultural management practices: (1) no-till (NT) followed by planting of winter wheat (Triticum aestivum), (2) NT followed by planting of blue lupin (Lupinus angustifolios L.), (3) maize crop residue (Zea mays L.) left on the surface, and (4) maize crop residue incorporated with tillage. Over a period of 139 days (from 15 June to 31 October 2013) the winter wheat cover crop produced a net accumulation of 257 g CO2-C m-2, while the tilled plot with no cover crop produced a net emission of 197 g CO2-C m-2 and the untilled plot with no cover emitted 235 g CO2-C m-2. The blue lupin cover crop emitted 58 g CO2-C m-2, indicating that winter cover crops can sequester carbon and reduce emissions over land left fallow through the non-growing season. The micrometeorological methods described in this work can detect significant differences between treatments over a period of a few months, an outcome important to determine which smallholder soil management practices can contribute towards mitigating climate change.