Few multiyear field studies have examined the impacts of a one‐time biochar application on net N mineralization and greenhouse gas emissions in an irrigated, calcareous soil; yet this use of biochar is hypothesized as a means of sequestering atmospheric CO2 and improving soil quality. We fall‐applied four treatments: stockpiled dairy manure (42 Mg ha−1 dry wt.), hardwood‐derived biochar (22.4 Mg ha−1), combined biochar and manure, and no amendments (control). Nitrogen fertilizer was applied in all plots and years based on treatment's preseason soil test N and crop requirements and accounting for estimated N mineralized from added manure. From 2009 to 2011, we measured greenhouse gas fluxes using vented chambers, net N mineralization using buried bags, corn (Zea mays L.) yield, and N uptake, and in a succeeding year, root and shoot biomass and biomass C and N concentrations. Both amendments produced persistent soil effects. Manure increased seasonal and 3‐yr cumulative net N mineralization, root biomass, and root/shoot ratio 1.6‐fold, CO2–C gas flux 1.2‐fold, and reduced the soil NH4/NO3 ratio 58% relative to no‐manure treatments. When compared with a class comprising all other treatments, biochar‐only produced 33% less cumulative net N mineralization, 20% less CO2–C, and 50% less N2O‐N gas emissions, and increased the soil NH4/NO3 ratio 1.8‐fold, indicating that biochar impaired nitrification and N immobilization processes. The multi‐year nature of biochar's influence implies that a long‐term driver is involved, possibly related to biochar's enduring porosity and surface chemistry characteristics. While the biochar‐only treatment demonstrated a potential to increase corn yields and minimize CO2–C and N2O‐N gas emissions in these calcareous soils, biochar also caused decreased corn yields under conditions in which NH4–N dominated the soil inorganic N pool. Combining biochar with manure more effectively utilized the two soil amendments, as it eliminated potential yield reductions caused by biochar and maximized manure net N mineralization potential.