Cultivation of winter wheat under reduced tillage systems is increasing in the U.S. Southern Great Plains. Likewise, there is revived interest for including summer legumes in monocultures of winter wheat as green sources of nitrogen (N). This study investigated the influence of tillage systems (no- and conventional tillage), and source and rates of N fertilizer (0, 45 and 90 kg N ha−1 yr−1 in inorganic N fertilizer, and cowpea as green manure) on emissions of carbon dioxide (CO2) and nitrous oxide (N2O) from winter wheat cultivation. The study was conducted within a long-term field experiment initiated in 2011, at upland and bottomland sites near El Reno, Oklahoma during the 2016–2017 growing season of winter wheat. The experiment was conducted site-wise as split-plots in a completely randomized design, with N treatment as main plots and tillage system as subplots. Thus, there were a total of eight treatment combinations with three replicated plots (4 m × 10 m) in each combination in both sites. Net ecosystem exchange (NEE) of CO2 was measured by a closed chamber connected to an infra-red gas analyzer, and fluxes were partitioned to gross primary production (GPP) and ecosystem respiration (ER). Heterotrophic soil respiration (SR) was measured on bare soil spots. Fluxes of N2O were measured with an opaque closed chamber system with a portable gas analyzer. Dynamics of canopy CO2 fluxes (NEE, GPP and ER) were similar between tillage systems, while canopy CO2 fluxes increased with rate of N fertilization. Canopy CO2 fluxes from cowpea and an unfertilized control were similar, and the lowest, due to poor growth of winter wheat compared to the N fertilized treatments. Fluxes of N2O approximated zero from all treatments throughout the study and no response of N fertilizer or tillage system was seen. In conclusion, the results from this study indicated that canopy fluxes of CO2 from winter wheat are controlled by forms and rates of N fertilizers rather than tillage systems.