Agricultural activities contribute to greenhouse gas emissions, but agroecosystems can also mitigate emissions by adding recalcitrant carbon sources such as biochar to soil. Our goal was to understand if greenhouse gas emissions decrease in soil amended with manure and biochar (MN) or with manure, nitrogen fertilizer, and biochar (MNB) than soil amended with manure and N fertilizer (MN) over the longer term. We hypothesized that biochar reduces the release of labile carbon and reactive nitrogen from organic amendments and nitrogen fertilizer, thereby reducing CO₂ and N₂O emissions and that soil temperature, moisture, and nitrogen availability are the strongest predictors for intra- and inter-annual variation in greenhouse gas emissions. Over three growing seasons, biweekly measurements of CO₂ and N₂O emissions were similar (P < 0.05) among treatments. Although input of labile carbon and reactive nitrogen was highest in MN and MB, cumulative CO₂ emissions were lowest (P < 0.05) in MNB. The availability of nitrogen from fertilizer caused greater cumulative N₂O emissions (P < 0.05) in MN and MNB. We found that soil temperature, moisture, and nitrogen availability regulated intraannual variability (P < 0.05) of CO₂ and N₂O emissions in all treatments, where emissions were greatest (P < 0.05) in the spring followed by summer and autumn. We accepted our hypothesis and concluded that, for cumulative emissions, biochar reduces the release of labile carbon and reactive nitrogen, but we rejected this hypothesis for biweekly emissions. We also concluded and accepted our hypothesis that soil temperature, moisture, and nitrogen availability regulated intraannual variation of CO₂ and N₂O in all treatments.