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This manuscript, Part II of a climate change impacts assessment series, describes changes in CO2, CH4, and N2O emissions and soil carbon storage on a theoretical farm in the Keremeos Creek watershed under scenarios of historical and potential climate using Holos v3.0.3 greenhouse gas (GHG) emissions model. The GENerate Earth SYstems Science input (GENESYS) spatial hydro-meteorological model outputs from Part I, which represent future hydro-meteorological conditions in the watershed under the ensemble averages of 15 General Circulation Models (GCMs) for two Representative Concentration Pathways (RCP) scenarios (RCP 4.5 and RCP 8.5) and three time periods (2011-2040, 2041-2070, and 2071-2100) relative to the 1961-1990 base period, are adapted to provide Holos v3.0.3 inputs. Adapting the GENESYS output facilitated Holos v3.0.3 modelling of farm GHG emissions to determine whether the simulated farm with both beef and crop production becomes a carbon sink, or source. The result demonstrated that there may be reductions in emissions related to enteric CH4, manure CH4, manure direct N2O, and indirect N2O for different climate change scenarios and time periods. However, there may also be increases in crop direct N2O and energy use CO2 for the same scenarios. Furthermore, soil carbon storage under fruit tree orchards is expected to increase. According to this result, the simulated farm in the Keremeos Creek watershed is a carbon sink and the carbon capture projects an increase to higher levels, depending on different climate change scenarios and time periods. However, if the simulation is conducted without fruit tree orchards as a carbon sink, the simulated farm in the Keremeos Creek watershed is a carbon source and the carbon emissions will increase for different climate change scenarios and time periods. These results demonstrate the importance of woody crops as a mitigation option for reducing farm-level GHG emissions in future.