The GreenFeed (GF; C-lock Inc.) system for estimating methane (CH4) and carbon dioxide emissions from cows enables data to be acquired from a grazing herd, where individuals are unencumbered by equipment associated with sampling respired breath. Cows choose when or if they want to visit a GF. Confidence in CH4 measurements from this system requires information on individual cow use, patterns of visits and data need to be accumulated over several days or weeks. The effect of stocking rate (SR) on CH4 and carbon dioxide emissions was examined in herds of 28 and 40 dairy cows, each grazing an 11-ha self-contained farmlet (Low SR and High SR), in four measurement periods over a lactation. Emissions were measured for up to 3 weeks in each period; CH4 averaged 331 and 305 g/cow.day, with 19.6 and 16.5 kg milk/cow.day during the measurements for the Low and High SR, respectively. Values for CH4 were similar to estimates derived from calculated feed intakes, and daily carbon dioxide emissions averaged 10.8 and 10.0 kg/day for cows in Low and High SR treatments, respectively. Data from the GF system distinguished effects of SR, but only ~20 cows from each farmlet were regular (daily) users, despite feed restrictions for the High SR cows. Visits by ‘users’ averaged 1.6 and 1.1 cows/h for Low and High SR herds, respectively, and were spread over 24 h with a small circadian variation in emission rates. The GF can be integrated into intensive pasture-based dairying and estimates of CH4 emissions are in line with expectations associated with feed availability and stage of lactation, however the variation between cows in number of visits to the GF has not been explained.