Epitaxial NbN/Al 2 O 3 /NbN trilayer structures with NbN thicknesses of 50−200 nm were grown by pulsed laser deposition. Within each trilayer configuration, it was observed that the top NbN layers exhibited slightly reduced crystallinity compared to the bottom NbN layers due to the strain-induced effects caused by the lattice mismatch between NbN and Al 2 O 3 . Notably, the trilayer structures exhibited epitaxial growth with consistent in-plane rotational orientations in the NbN layers. Significant deviations in the stoichiometry of the NbN layers were detected, primarily stemming from N-deficient and O-rich regions. Moreover, the chemical non-uniformity within the NbN layers intensified as the layer thickness decreased. The lateral N/Nb distribution showed a complementary distribution with O/Nb, resulting from a higher tendency for NbO x formation with lower NbN thicknesses. To gain a deeper understanding of the formation and impacts of local point defects, such as nitrogen vacancies and oxygen impurities, density functional theory (DFT) calculations were employed. The obtained defect formation energies suggest that O substitutional defects will prevail in an oxygen-rich environment over N vacancies. The investigation further explored the role of these defects in tuning the electronic states at the Fermi level.