Heteroepitaxy offers a new type of control mechanism for the crystal structure, the electronic correlations, and thus the functional properties of transition-metal oxides. Here, we combine electrical transport measurements, high-resolution scanning transmission electron microscopy (STEM), and density functional theory (DFT) to investigate the evolution of the metal-to-insulator transition (MIT) in NdNiO$_3$ films as a function of film thickness and NdGaO$_3$ substrate crystallographic orientation. We find that for two different substrate facets, orthorhombic (101) and (011), modifications of the NiO$_6$ octahedral network are key for tuning the transition temperature $T_{text{MIT}}$ over a wide temperature range. A comparison of films of identical thickness reveals that growth on [101]-oriented substrates generally results in a higher $T_{text{MIT}}$, which can be attributed to an enhanced bond-disproportionation as revealed by the DFT+$U$ calculations, and a tendency of [011]-oriented films to formation of structural defects and stabilization of non-equilibrium phases. Our results provide insights into the structure-property relationship of a correlated electron system and its evolution at microscopic length scales and give new perspectives for the epitaxial control of macroscopic phases in metal-oxide heterostructures.