Superconducting qubits have arisen as a leading technology platform for quantum computing which is on the verge of revolutionizing the world’s calculation capacities. Nonetheless,the fabrication of computationally reliable qubit circuits requires increasing the quantum coherence lifetimes, which are predominantly limited by the dissipations of two-level system (TLS) defects present in the thin superconducting film and the adjacent dielectric regions. In this paper, we demonstrate the reduction of two-level system losses in three-dimensional superconducting radio frequency (SRF) niobium resonators by atomic layer deposition (ALD) of a 10 nm aluminum oxide Al2O3 thin films followed by a high vacuum (HV) heat treatment at 650 °C for few hours. By probing the effect of several heat treatments on Al2O3-coated niobium samples by X-ray photoelectron spectroscopy (XPS) plus scanning and conventional high resolution transmission electron microscopy (STEM/HRTEM) coupled with electron energy loss spectroscopy (EELS) and (EDX) , we witness a dissolution of niobium native oxides and the modification of the Al2O3-Nb interface, which correlates with the enhancement of the quality factor at low fields of two 1.3 GHz niobium cavities coated with 10 nm of Al2O3.