The effects of crop production practices on fluxes of greenhouse gases from soil are not fully understood. Gas fluxes were measured from a field plot study involving the variables of tillage, crop rotation, N fertilizer, and cover crop. Fluxes of greenhouse gases were measured by gas chromatography bi-weekly during the growing season. Emission of N2O and uptake of CH4 were decreased when soils were under no-tillage (NT) compared to minimum tillage (MT). Nitrogen fertilizer, however, significantly increased emission of N2O from the soil for more than one month after application. Emission of N2O from the soybean (Glycine max) plots was more than from corn (Zea mays) plots except for the period after application of N fertilizer in the corn plots. Emission of CO2 from plots with cover crops was increased, especially in early spring, and emission of N2O and uptake of CH4 were decreased as compared with plots without cover crops. Fluxes of CO2 from soil were not significantly impacted by fertilizer applications, different crops and different tillage systems.