Land management practices and cropping strategies significantly affect greenhouse gas (GHG) emissions from soil gas flux. Managing soils to mitigate GHG emissions has been the focus of several studies in recent years. However, knowledge regarding the effects of land management on soil GHG emissions in the Missouri River floodplain (MRF) is scarce. This study evaluated soil carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) emissions among conventional and alternative land use types in the MRF. Soil GHG emissions from three land use systems, corn–soybean rotation (AG), tree/grass agroforestry (AF), and riparian forest (RF) were investigated over the growing season. Mean cumulative soil GHG emissions from AF, RF, and AG over the two-year study period reached 6, 4, and 3 Mg CO2-C ha-1 yr-1 carbon dioxide equivalent (CO2eq), respectively. Fertilizer application and soil saturation conditions after flooding events were the key drivers of soil N2O and CH4 emissions. No flooding occurred in the RF system, and this area remained a CH4 sink during the study period. A peak in CH4 flux in the AF and AG treatments was observed after flooding events. In floodplain land use systems, opportunities exist to mitigate soil GHG emissions and CO2eq by reducing N fertilizer application. With a wider vision focused on GHG emissions from the current and possible alternative land uses in the MRF, the output of this study gives a measure to assist in the development of integrated solutions and policies regarding climate change mitigation at the local scale.