The effect of pile mixing on greenhouse gas (GHG) emissions during dairy manure composting was determined using large flux chambers designed to completely cover replicate pilot-scale compost piles. GHG emissions from compost piles that were mixed four times during the 80 day trial were approximately 20% higher than emissions from unmixed (static) piles. For both treatments, carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) accounted for 75–80%, 18–21%, and 2–4% of GHG emissions, respectively. Seventy percent of CO2 emissions and 95% of CH4 emissions from all piles occurred within first 23 days. By contrast, 80–95% of N2O emissions occurred after this period. Mixed and static piles released 2 and 1.6 kg GHG (CO2-Eq.) for each kg of degraded volatile solids (VS), respectively. Our results suggest that to minimize GHG emissions, farmers should store manure in undisturbed piles or delay the first mixing of compost piles for approximately 4 weeks.