In this study, we evaluated the short-term dynamics of carbon dioxide net ecosystem exchange (NEE) resulting from diversifying corn-soybean rotations with winter wheat (WW) and cover crops (CC). The experiment was conducted on non-diverse (corn-soybean-soybean) and diverse (corn/CC-soybean-WW/CC) rotation fields over a three-year period. Overall, the diverse rotation significantly enhanced gross primary productivity– the carbon (C) uptake component of NEE (–3507±34 g C m-2) compared to the non-diverse rotation (–2789±45 g C m-2) but was accompanied by increased respiration– the C loss component of NEE in the diverse field (2836±38 g C m-2) than in the non-diverse field (2237±38 g C m-2). Results from this study showed that management practices such as crop diversification can induce C uptake in cropland but at the cost of increased C loss via respiration. Long term studies will be needed to further establish this NEE trend from diversified farming.