Atomic layer deposition (ALD) of high-κ dielectrics on two-dimensional (2D) materials (including graphene and transition metal dichalcogenides) still represents a challenge due to the lack of out-of-plane bonds on the pristine surfaces of 2D materials, thus making the nucleation process highly disadvantaged. The typical methods to promote the nucleation (i.e., the predeposition of seed layers or the surface activation via chemical treatments) certainly improve the ALD growth but can affect, to some extent, the electronic properties of 2D materials and the interface with high-κ dielectrics. Hence, direct ALD on 2D materials without seed and functionalization layers remains highly desirable. In this context, a crucial role can be played by the interaction with the substrate supporting the 2D membrane. In particular, metallic substrates such as copper or gold have been found to enhance the ALD nucleation of Al2O3 and HfO2 both on monolayer (1 L) graphene and MoS2. Similarly, uniform ALD growth of Al2O3 on the surface of 1 L epitaxial graphene (EG) on SiC (0001) has been ascribed to the peculiar EG/SiC interface properties. This review provides a detailed discussion of the substrate-driven ALD growth of high-κ dielectrics on 2D materials, mainly on graphene and MoS2. The nucleation mechanism and the influence of the ALD parameters (namely the ALD temperature and cycle number) on the coverage as well as the structural and electrical properties of the deposited high-κ thin films are described. Finally, the open challenges for applications are discussed.