The mechanical properties of engineered van der Waals (vdW) 2D materials and heterostructures are critically important for their implementation into practical applications. Using a non-destructive Raman spectroscopy approach, this study investigates the strain evolution of single-layer graphene (SLGr) and few-layered boron nitride/graphene (FLBN/SLGr) heterostructures. The prepared 2D materials are synthesized via chemical vapor deposition (CVD) method and then transferred onto flexible polyethylene terephthalate (PET) substrates for subsequent strain measurements. For this study, a custom-built mechanical device-jig is designed and manufactured in-house to be used as an insert for the 3D piezoelectric stage of the Raman system. In situ investigation of the effects of applied strain in graphene detectable via Raman spectral data in characteristic bonds within SLGr and FLBN/SLGr heterostructures is carried out. The in situ strain evolution of the FLBN/SLGr heterostructures is obtained in the range of (0–0.5%) strain. It is found that, under the same strain, SLG exhibits a higher Raman shift in the 2D band as compared with FLBN/SLGr heterostructures. This research leads to a better understanding of strain dissipation in vertical 2D heterostacks, which could help improve the design and engineering of custom interfaces and, subsequently, control lattice structure and electronic properties. Moreover, this study can provide a new systematic approach for precise in situ strain assessment and measurements of other CVD-grown 2D materials and their heterostructures on a large scale for manufacturing a variety of future micro- and nano-scale devices on flexible substrates.