In this paper, we present a study of tungsten disulfide (WS2) two-dimensional (2D) crystals, grown on epitaxial Graphene. In particular, we have employed scanning electron microscopy (SEM) and µRaman spectroscopy combined with multifunctional scanning probe microscopy (SPM), operating in peak force–quantitative nano mechanical (PF-QNM), ultrasonic force microscopy (UFM) and electrostatic force microscopy (EFM) modes. This comparative approach provides a wealth of useful complementary information and allows one to cross-analyze on the nanoscale the morphological, mechanical, and electrostatic properties of the 2D heterostructures analyzed. Herein, we show that PF-QNM can accurately map surface properties, such as morphology and adhesion, and that UFM is exceptionally sensitive to a broader range of elastic properties, helping to uncover subsurface features located at the buried interfaces. All these data can be correlated with the local electrostatic properties obtained via EFM mapping of the surface potential, through the cantilever response at the first harmonic, and the dielectric permittivity, through the cantilever response at the second harmonic. In conclusion, we show that combining multi-parametric SPM with SEM and µRaman spectroscopy helps to identify single features of the WS2/Graphene/SiC heterostructures analyzed, demonstrating that this is a powerful tool-set for the investigation of 2D materials stacks, a building block for new advanced nano-devices.