Manure and fertilizer applications contribute to greenhouse gas (GHG) and ammonia (NH3) emissions. Losses of NH3 and nitrous oxide (N2O) are an economic loss of nitrogen (N) to farms, and methane (CH4), N2O, and carbon dioxide (CO2) are important GHGs. Few studies have examined the effects of low-disturbance manure incorporation (LDMI) on both NH3 and GHG fluxes. Here, NH3, N2O, CH4, and CO2 fluxes in corn (Zea mays L.)-winter rye (Secale cereale L.) field plots were measured under fall LDMI (aerator/band, coulter injection, strip-till, sweep inject, surface/broadcast application, broadcast-disk) and spring-applied urea (134 kg N ha(-1)) treatments from 2013 to 2015 in central Wisconsin. Whereas broadcast lost 35.5% of applied ammonium-N (NH4-N) as NH3-N, strip-till inject and coulter inject lost 0.11 and 4.5% of applied NH4-N as NH3, respectively. Mean N2O loss ranged from 2.7 to 3.6% of applied total N for LDMI, compared with 4.2% for urea and 2.6% for broadcast. Overall, greater CO2 fluxes for manure treatments contributed to larger cumulative GHG fluxes compared with fertilizer N. There were few significant treatment effects for CH4 (P > .10); however, fluxes were significantly correlated with changes in soil moisture and temperature. Results indicate that LDMI treatments significantly decreased NH3 loss but led to modest increases in N2O and CO2 fluxes compared with broadcast and broadcast-disk manure incorporation. Tradeoffs between N conservation versus increased GHG fluxes for LDMI and other methods should be incorporated into nutrient management tools as part of assessing agri-environmental farm impacts.