Calibration and validation are standardized practices to establish the credibility of biogeochemical models for understanding agroecosystem nutrient dynamics. We evaluated three automatic calibration approaches, including simultaneous, sequential, and separate, for the calibration of model parameters of the biogeochemical DeNitrification DeComposition (DNDC) model through inverse modeling using PEST, open-source parameter estimation, and uncertainty analysis software. While manual calibration by experts performed the best during calibration period, followed by simultaneous calibration, sequential calibration had the best model performance during the validation period. Model sensitivity analyses demonstrated water leaching to be sensitive to curve number and drain spacing, nitrate leaching to be sensitive to porosity and clay content, and corn yield to be sensitive to accumulative temperature and grain C/N ratio. While some level of expertise is required to inform the automated calibration procedure, it represents a more efficient and robust approach toward increasing the performance of biogeochemical models.