The monitoring of moisture levels and the investigation of the dielectric properties of materials are tasks that can be suitably performed through Time Domain Reflectometry (TDR) techniques. In particular, moisture monitoring of granular agro-foods is a major interest for several industrial applications. Despite the extensive literature regarding the use of TDR technology, the state of the art is lacking in a rigorous metrological characterization of the results achieved, especially for the agro-foods area. To fill this gap, in this paper the Authors carry out a comparative analysis between moisture content measurements obtained through two different TDR instruments on various granular materials. First, the major error contributions affecting the overall performance of the TDR-based method are discussed; in particular, the error contributions that are intrinsic in the method are discriminated from those related to the specific experimental conditions. Successively, systematic errors effects are minimized through a preliminary calibration procedure of the experimental set-up. Finally, results are compared and analyzed through a statistical approach, providing both an assessment of the repeatability of measurements and a rigorous metrological characterization. This ultimately leads to a performance characterization, particularly useful for practical industrial applications.