Microstructural study of cement and its composites has immense significance from both fundamental and applied research points of view. Concrete, a mesoscale cementitious material, possesses high heterogeneity and inherent complex behavior. The multi-phases of concrete show an evolving nature at any instance of time, starting from the initiation of hydration to the complete maturity level. The hydration products and the aggregate-matrix Interfacial Transition Zone (ITZ) play a crucial role in defining the microstructural arrangement, which determines the mechanical and durability properties. Ultrasonic diffusion-based study has a unique advantage for characterising microstructural behavior in heterogeneous materials as it can decouple the different attenuating parameters- diffusivity (D) and dissipation (σ), where, D reflects the material microstructure and σ indicates the viscoelastic property of the base material. For that purpose, an ultrasonic diffusion study has been carried out in the present research for hydration monitoring in two scales, cement (micro-scale), and concrete (meso-scale) under different transmission modes. Ultrasonic measurements have been processed in the time-frequency domain to deduce the diffusivity and dissipation parameters using Spectral Energy Density distribution over the entire time window. The present research reveals the key findings as follows: (1) the influence of microstructure in ultrasonic wave propagation can be explicitly demonstrated using diffusion based analytical formulation and experimental results; (2) ultrasonic parameters (in terms of diffusivity and dissipation) can provide physical information on microstructural development in cementitious material during its hydration stage; and (3) the diffusion based method can distinguish the complex microstructural behavior across the scales of heterogeneity- micro-scale (cement paste) to meso-scale (concrete).