Methods and systems for calibrating quantum processors are discussed. A model of a portion of the processor to be calibrated has one or more determinable parameters and an uncertainty for the determinable parameter(s). A measurement procedure is iteratively performed by selecting a subset of possible measurements and generating predicted measurement outcomes and predicted uncertainties for the determinable parameter for each measurement in the subset of possible measurements. Based on the predicted reduction in uncertainty for the determinable parameter, one or more measurements is selected. Instructions are transmitted to the quantum processor to perform the selected measurements, and the results are returned to update the model of the portion of the processor to be calibrated. Once a termination criteria is met, a calibrated value is generated for the determinable parameter. Compensating signals can be applied to devices of the quantum processor to calibrate the devices.