In this paper, the atomic layer deposition (ALD) of ultra-thin films (<4 nm) of Al2O3 and HfO2 on gold-supported monolayer (1L) MoS2 is investigated, providing an insight on the mechanisms ruling the nucleation in the early stages of the ALD process. A preliminary multiscale characterization of large area 1L-MoS2 exfoliated on sputter-grown Au/Ni films demonstrated: (i) a tensile strain (from 0.1 to 0.3%) and p-type doping (from 1 × 1012 to 4 × 1012 cm−2) distribution at micro-scale; (ii) an almost conformal MoS2 membrane to the Au grains topography, with some locally detached regions, indicating the occurrence of strain variations at the nanoscale; (iii) atomic scale variability (from ∼ 4.0 to ∼ 4.5 Å) in the Mo-Au atomic distances was detected, depending on the local configuration of Au nanograins. Ab initio DFT calculations of a free-standing MoS2 layer and a simplified MoS2/Au(111) interface model showed a significant influence of the Au substrate on the MoS2 energy band structure, whereas small differences were accounted for the adsorption of H2O, TMA (co-reactant, and Al-precursor, respectively) molecules, and a slight improved adsorption was predicted for TDMAHf (Hf-precursor). This suggests a crucial role of nanoscale morphological effects, such as the experimentally observed local curvature and strain of the MoS2 membrane, in the enhanced physisorption of the precursors. Afterwards the nucleation and growth of Al2O3 an HfO2 films onto 1L-MoS2/Au was investigated in detail, by monitoring the surface coverage as a function of the number (N) of ALD cycles, with N from 10 to 120. At low N values, a slower growth rate of the initially formed nuclei was observed for HfO2, probably due to the bulky nature of the TDMAHf precursor as compared to TMA. On the other hand, the formation of continuous films was obtained in both cases for N > 80 ALD cycles, corresponding to ∼ 3.6 nm Al2O3 and ∼ 3.1 nm HfO2. Current mapping on these ultra-thin films by conductive-AFM showed, for the same applied bias, a uniform insulating behavior of Al2O3 and the occurrence of few localized breakdown spots in the case of HfO2, associated to a less compact films regions. Finally, an increase of the 1L-MoS2 tensile strain was observed by Raman mapping after encapsulation with both high-κ films, accompanied by a reduction in the PL intensity, explained by the effects of strain and the higher effective dielectric constant of the surrounding environment.