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 such applications are hypothesized as a means of sequestering atmospheric CO2 and improving soil quality. We fall-applied four treatments, stockpiled dairy manure (42 Mg/ha dry wt.); hardwood-derived biochar (22.4 Mg/ha); combined biochar and manure; and no amendments (control). Nitrogen fertilizer was applied in all plots and years based on treatment’s pre-season 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 (NNM) using buried bags, corn yield, and N uptake, and in a succeeding year, root and shoot biomass and biomass C and N concentrations. Both amendments produced soil produced persistent soil effects. Manure increased seasonal and three year cumulative NNM, root biomass, and root:shoot ratio 1.6-fold, CO2-C gas flux 1.2-fold, and reduced soil NH4:NO3 ratio 58% relative to no-manure treatments. Relative to all other treatments on average, biochar-only produced 33% less cumulative NNM, 20% less CO2-C and 50% less N2O-N gas emissions, 35% less root biomass, and increased soil NH4:NO3 ratio 1.8-fold. These long-term effects suggest that biochar slightly impaired nitrification and N immobilization processes, and are likely caused by enduring biochar porosity and surface chemistry characteristics that influence N-transform-ation processes, alter microbial populations, and sequester soil ammonium. 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 certain soil nutrient conditions. Combining biochar with manure effectively utilizes these soil amendments as it eliminated potential yield reductions and maximized manure net N mineralization potential.