The effect of N source (digestate and raw dairy manure) and application timing (spring- and fall-applied) on nitrous oxide (N2O) emissions and nitrate (NO3) leaching was evaluated. These N sources, as well as urea, were incorporated into plots with contrasting soil textures (sandy-loam vs. clay). Measurements of leached NO3 and N2O fluxes were collected using a tile drainage system, zero-tension lysimeters, and chambers, respectively. N2O flux measurements were also used to validate the agro-ecosystem model, DAYCENT. Overall, there was no difference in N2O emissions between N sources in the clay field but digestate had significantly higher N2O emissions than raw dairy manure in the sandy-loam field. Treatments with lower N2O emissions tended to have higher NO3 leaching. There was no overall effect of timing on N2O emissions, but fall applications had higher NO3 leaching. DAYCENT’s effectiveness at simulating N2O fluxes could be improved to better assess management practices.