Manure application influences ammonia (NH₃) and greenhouse gas emissions; however, few studies have quantified the effects of manure application methods and timing on NH₃, nitrous oxide (N₂O), carbon dioxide (CO₂), and methane (CH₄) fluxes simultaneously. We evaluated surface-applied liquid manure application with disk incorporation versus injection on NH₃, N₂O, CO₂, and CH₄ fluxes in central Wisconsin corn silage (Zea mays L.) plots during pre-plant (PP) and sidedress (SD) application windows from 2009 to 2011. Manure treatments were PP injection (PP-Inject) and injection at sidedress time (SD-Inject) to growing corn, along with two incorporation times for PP surface application (within 24 h—PP-1-hr; within 3 days—PP-3-day). Mean NH₃ emissions were 95% lower for injected treatments compared to surface application in both years, with larger losses for PP-3-day and SD-Surf. While N₂O fluxes were generally low, larger increases after manure application were associated with injection and triggered by soil moisture/temperature changes. Mean CO₂ and CH₄ were unaffected by manure treatments and influenced more by weather. Overall, injection conserved more available soil N while contributing to modest N₂O emission, suggesting manure injection may offer greater agri-environmental benefits on the whole over surface application.