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Accurate measurement of dielectric properties of granular materials and powders is important in material science, pharmacology, agriculture, and other fields. Granular materials present a wide range of measurement challenges not encountered with solid and liquid samples. This paper presents the calibration process for measurement of granular material properties using a custom-designed dielectric spectroscopy system. The process uses systematic iterative calibration for the individual stages of the measurement circuit, the calibration of the sensor fixture, and the determination of a frequency-dependent phase-shift due to the operational amplifiers in the circuit. The results show that using the calibrated system to measure the air's relative dielectric permittivity noticeably reduces measurement deviation to 0.5%, from more than 30% in non-calibrated mode. Based on the material dielectric signature acquired in the frequency domain, the measurement system can be used to identify a broad variety of granular materials. Since allowing direct contact with the sensor electrodes is undesirable for some materials, this paper demonstrates how insulating the granular material in a thin film during material property measurement can be taken into account.