AbstractThis long‐term study was established to increase knowledge of greenhouse gas (GHG) emissions from irrigated cropping systems utilizing dairy manure solids and compost in semiarid southern Idaho. The objective of this field study was to determine the effect of synthetic N fertilizer (urea or SuperU [enhanced‐efficiency synthetic fertilizer]), composted dairy manure, dairy manure (fall or spring applied), and a control (no fertilizer or manure) on nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) emissions over the growing season. The fertilizer and manure treatments were not applied to alfalfa (Medicago sativa L.) (2017) but were applied to corn (Zea mays L.) (2018; except SuperU) and barley (Hordeum vulgare L.) (2019). Cumulative N2O losses over the 3 yr ranged from 2.8 to 5.2 kg N2O‐N ha–1, with the fall and spring manure emitting the greatest amounts of N2O. Emission factors indicated that up to 0.79% of the total N applied was lost as N2O‐N during the growing seasons. Cumulative losses of CO2 and CH4 across the rotation were on average 12,170 kg CO2–C ha–1 and –0.77 kg CH4–C ha–1, respectively, with no significant differences among the treatments. Major N2O pulses were associated with early‐season irrigation events and incorporation of fertilizer and manure, but overall fluxes tended to be the greatest when soil temperatures were higher. Dairy manure and compost applications were also found to cause rapid and significant increases in soil organic carbon (SOC) in the top 30 cm of soil under corn and barley. Despite the fact that manure does cause elevated soil N2O emissions, it should be considered as an alternative to synthetic fertilizer use due to its ability to increase SOC and potentially help reduce the global warming potential.