An auto-calibration controller configured to automatically tune a dosing unit of an aftertreatment system. The auto-calibration controller is configured to command the dosing unit to dose reductant at a first dosing command rate at a first input pressure value based on a dosing command value of a dosing command table. The auto-calibration controller is further configured to interpret a parameter indicative of an actual amount of dosed reductant by the dosing unit and compare the actual amount of dosed reductant to an expected amount of dosed reductant. The auto-calibration controller is further configured to update the dosing command value of the dosing command table of a control module of the aftertreatment system responsive to the comparison of the actual amount of dosed reductant to the expected amount of dosed reductant.