This paper presents an investigation of energy dissipation of vibrating binary powder mixtures packed naturally at low acceleration levels. A model based upon both viscoelastic and two-phase theories has been developed to predict the dissipation energy of binary mixtures packed naturally. Two experimental systems including open-top and top-cap systems were used to measure the properties of the mixture beds subject to vibration. The open-top system provides the dissipation energy rate of a powder bed packed naturally. On the other hand, the top-cap system produces the elastic and damping properties of a powder bed with a top-cap mass as a loading weight. The model developed uses the elastic and damping properties of the powder bed deduced from the top-cap data to predict the properties of beds packed naturally. Comparison between the model and experimental data obtained by the open-top system has been made, and good agreement between the model prediction and the experimental data was obtained. This has implications for the damping mechanisms and dynamics of binary powder mixtures packed naturally under vibration.