Herbicides are used to control weeds in agricultural crops such as alfalfa (Medicago sativa L.), which is a forage crop. It is unclear what, if any, effect herbicides have on greenhouse gas (GHG) emissions when used on alfalfa. Our study was conducted in 2017 and 2018 to investigate the effects of two herbicides (Quizalofop-p-ethyl, QE and Bentazone, BT) on methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) emissions from soil planted with alfalfa. QE is used to control grasses and BT is used for broadleaf weed control. Soil CO2 emissions and soil uptake of CH4 increased significantly in both years following the QE and BT treatments, although CO2 emissions differed significantly between the trial years. N2O emissions decreased relative to the control and showed no significant differences between the trial years. The application of QE and BT on alfalfa resulted in a significant increase in CO2 emissions which contributed to a significant increase in GHG emissions. The application of QE influenced GHG emissions more than BT. We demonstrated the potential effect that herbicide applications have on GHG fluxes, which are important when considering the effect of agricultural practices on GHG emissions and the potential for global warming over the next 100 years.