Methane (CH) and carbon dioxide (CO) represent 11 and 81%, respectively, of all anthropogenic greenhouse gas emissions. Agricultural CH emissions account for approximately 43% of all anthropogenic CH emissions. Most agricultural CH emissions are attributed to enteric fermentation within ruminant livestock; hence, the heightened interest in quantifying and mitigating this source. The automated, open-circuit gas quantification system (GQS; GreenFeed, C-Lock, Inc., Rapid City, SD) evaluated here can be placed in a pasture with grazing cattle and can measure their CH and CO emissions with spot sampling. However, improper management of the GQS can have an erroneous effect on emission estimates. One factor affecting the quality of emission estimates is the airflow rates through the GQS to ensure a complete capture of the breath cloud emitted by the animal. It is hypothesized that at lower airflow rates this cloud will be incompletely captured. To evaluate the effect of airflow rate through the GQS on emission estimates, a data set was evaluated with 758 CO and CH emission estimates with a range in airflows of 10.7 to 36.6 L/s. When airflow through the GQS was between 26.0 and 36.6 L/s, CO and CH emission estimates were not affected ( = 0.14 and 0.05, respectively). When airflow rates were less than 26.0 L/s, CO and CH emission estimates were lower and decreased as airflow rate decreased ( < 0.0001). We hypothesize that when airflow through the GQS decreases below 26 L/s, breath capture was incomplete and CO and CH emissions are underestimated. Maintaining mass airflow through a GQS at rates greater than 26 L/s is important for producing high quality CO and CH emission estimates.