Calibrating the operation of a cutter used in a portioning system to cut workpieces into portions, wherein the work- piece is carried along a driven conveyance device past a scanner and then to a cutting apparatus. The calibration method employs a correction algorithm to correct for vari- ables or limitations in the condition of one or more com- ponents of the portioning system and/or variations or limi- tations in the operation or operational capabilities of the portioning system. The correction algorithm may also factor in the physical condition, configuration, or composition of the workpieces being portioned, as well as whether the workpieces move on the conveyance device prior to and/or during the portioning operation.