A calibration system is provided for an oven controlled MEMS oscillator. The calibration system includes control circuitry that to separately selects predetermined target set-point values and controls a heater inside the oven controlled MEMS oscillator based on each of the selected target set-point values to adjust a set-point of the oven controlled MEMS oscillator. The system further includes an oscillation measurement circuit that measures respective oscillation frequencies at each adjusted set-point corresponding to each of the selected predetermined target set-point values. The measured oscillation frequencies can then be used to determine a target set-point operation value for the oven controlled MEMS oscillator, which can be sued to calibrate the oven controlled MEMS oscillator.