Flux data from agricultural systems improves our understanding of the carbon exchange between the soil and atmosphere related to changes in soil organic matter, greenhouse gas emissions and sequestration. Changes in cropping systems have the potential to affect the carbon balance, especially if perennial crops are converted to annual crops. We studied this process by following the land-conversion procedure done by an agricultural producer in southern Manitoba, Canada. Three eddy covariance towers were installed in 2009 to measure net CO₂ ecosystem exchange over a perennial forage field (control) and two recently-converted fields. One converted field was tilled in 2008, and had oats-canola-oats planted in consecutive years. A second converted field was tilled in 2009. The control field was a long-term perennial pasture dominated by grasses. Conversion caused an immediate carbon loss following tillage and the subsequent annual crop has large spring and fall carbon losses when crops are not present. Ecosystem carbon budgets that include harvest removals showed net carbon losses by the annual crops and closer to carbon neutrality for the perennial crop. Excess moisture contributed to variability among sites, as did weed growth after harvest, and each site showed inter-annual variability depending on weather, crop, and management.