Crop canopy CO2 exchange rate (CER) includes crop photosynthesis and soil/plant respiration. A portable canopy chamber is effective in determining crop CER values at a relatively small spatial (m2) scale. The objectives of this study were to use a canopy chamber to measure CO2 fluxes in corn (Zea mays L.) and soybean [Glycine max (L.) Merr.]. Chamber measurements were performed for 18 and 15 d in 2013 and 2014, respectively. The canopy chamber measures instantaneous CER fluxes, and daily and daytime cumulative CO2 values were calculated from the instantaneous CER. The chamber CER results were compared with nearby eddy covariance (EC) flux tower measurements at a variety of time scales, i.e., instantaneous, daily, and daytime cumulative (multiple months). The daily and daytime cumulative chamber CER values were within 5% of the EC results, providing evidence for the effectiveness of the portable canopy chamber method. In conclusion, the portable canopy chamber provides reliable CO2 flux measurements despite the small size of field plots.