Organic crop production is increasing with consumer demand, but research is needed on the best management practices that minimize greenhouse gas (GHG) emissions. This study was conducted in central Missouri from 2012 to 2014 using a 3-yr rotation, consisting of corn (Zea mays L.), cereal rye cover crop (Secale cereale L.), soybean (Glycine max L.), winter wheat (Triticum aestivum L.), summer cover crop mix [Buckwheat (Fagopyrum esculentum Moench), sunn hemp (Crotalaria juncea L.), cowpea (Vigna unguiculata (L.) Walp.)], and cereal rye/hairy vetch cover crop mix (Vicia villosa L.). Treatments included tillage/cover crop practice (TCCP) combinations: (i) tillage with no cover crop (TNCC), (ii) tillage with cover crop (TCC), and (iii) no-till with cover crop (NTCC) and compost additions relative to the recommended rate (0x, 1x, 1.5x). Carbon dioxide (CO2) and nitrous oxide (N2O) emission measurements followed GRACEnet protocol. GHG emissions were not influenced by management practices in 2012 due to severe drought. TCCP had direct (2013 corn, 2014 soybean) or interactive (2014 wheat) effects on CO2 emissions; compost had a direct effect (2014 corn) on N2O emissions. Drought in 2012 and 2013 contributed to generally low CO2 and N2O emissions (99-2924 kg CO2-C ha(-1) and 0-0.8 kg N2O-N ha(-1), respectively) while emissions increased in 2014 (527-7740 kg CO2-C ha(-1) and < 0.1-10.1 kg N2O-N ha(-1), respectively). Across all years and crops, NTCC showed greater CO2 emissions than TNCC (1579 and 893 kg CO2-C ha(-1), respectively). While few treatment differences were observed, TCCP resulted in more GHG emission differences than compost rate.