Diversifying agronomic production systems by combining crops and livestock (i.e., Integrated Crop Livestock systems; ICL) may help mitigate the environmental impacts of intensive single-commodity production. In addition, harvesting row-crop residues and/or perennial biomass could increase the multi-functionality of ICL systems as a potential source for second-generation bioenergy feedstock. Here, we evaluated non-CO2 soil greenhouse gas (GHG) emissions from both row-crop and perennial grass phases of a field-scale model ICL system established on marginally productive, poorly drained cropland in the western US Corn Belt. Soil emissions of nitrous oxide (N2O) and methane (CH4) were measured during the 2017–2019 growing seasons under continuous corn (Zea mays L.) and perennial grass treatments consisting of a common pasture species, ‘Newell’ smooth bromegrass (Bromus inermis L.), and two cultivars of switchgrass (Panicum virgatum L.), ‘Liberty’ and ‘Shawnee.’ In the continuous corn system, we evaluated the impact of stover removal by mechanical baling vs. livestock grazing for systems with and without winter cover crop, triticale (x Triticosecale neoblaringhemii A. Camus; hexaploid AABBRR). In perennial grasslands, we evaluated the effect of livestock grazing vs. no grazing. We found that (1) soil N2O emissions are generally higher in continuous corn systems than perennial grasslands due to synthetic N fertilizer use; (2) winter cover crop use had no effect on total soil GHG emissions regardless of stover management treatment; (3) stover baling decreased total soil GHG emissions, though grazing stover significantly increased emissions in one year; (4) grazing perennial grasslands tended to increase GHG emissions in pastures selected for forage quality, but were highly variable from year to year; (5) ICL systems that incorporate perennial grasses will provide the most effective GHG mitigation outcomes.