The magnetotransport properties of spin valve structure are highly influenced by the type of intervening layer inserted between the ferromagnetic electrodes. In this scenario, spin filtering effect at the interfaces plays a crucial role in determining the magnetoresistance (MR) of such magnetic structures, which can be enhanced by using a suitable intervening layer. Here, the authors investigate the spin filtering effect of the two‐dimensional layers such as hexagonal boron nitride (hBN), graphene (Gr), and Gr‐hBN hybrid system for modifying the magnetotransport characteristics of the vertical spin valve architectures (Ni/hBN/Ni, Ni/Gr/Ni, and Ni/Gr‐hBN/Ni). Compared to graphene, hBN incorporated magnetic junction reveals higher MR and spin polarizations (P) suggesting better spin filtering at the interfaces. The MR for hBN incorporated junction is calculated to be ≈0.83%, while that of graphene junction it is estimated to be ≈0.16%. Similar contrast is observed in the ‘P’ of ferromagnets (FMs) for the two junctions, that is, ≈6.4% for hBN based magnetic junction and ≈2.8% for graphene device. However, for Gr‐hBN device, the signal not only get inverts, but it also suggests efficient spin filtering mechanism at the FM interfaces. Their results can be useful to comprehend the origin of spin filtering and the choice of non‐magnetic spacer for magnetotransport characteristics. The authors investigate spin filtering mechanism by incorporating 2D materials in spin valve devices. Comparing to graphene, hBN device reveals pronounced spintronic features suggesting better spin filtering at the interfaces. Furthermore, graphene and hBN incorporated magnetic junctions reveal positive MR, while that for Gr‐hBN heterostructure the signal not only becomes negative, but also facilitates efficient spin filtering at the interfaces.