Systems for transport and processing of granular media are challenging to analyse, operate and optimise. In the mining and mineral processing industries, these systems are chains of processes with a complex interplay among the equipment, control and processed material. The material properties have natural variations that are usually only known at certain locations. Therefore, we explored a material-oriented approach to digital twins with a particle representation of the granular media. In digital form, the material is treated as pseudo-particles, each representing a large collection of real particles of various sizes, shapes and mineral properties. Movements and changes in the state of the material are determined by the combined data from control systems, sensors, vehicle telematics and simulation models at locations where no real sensors could see. The particle-based representation enables material tracking along the chain of processes. Each digital particle can act as a carrier of observational data generated by the equipment as it interacts with the real material. This make it possible to better learn the material properties from process observations and to predict the effect on downstream processes. We tested the technique on a mining simulator and demonstrated the analysis that can be performed using data from cross-system material tracking.