Shadowing effects during the growth of nano-and microstructures are crucial for the realization of several technological applications. They are given by the shielding of the incoming material flux provided by the growing structures themselves. Their features have been deeply investigated by theoretical approaches, revealing important information to support experimental activities. However, comprehensive investigations able to follow every stage of the growth processes as a whole, particularly useful to design and understand targeted experiments, are still challenging. In this work, we study the thin-film growth dynamics by means of a diffuse interface approach accounting for both deposition with shadowing effects and surface diffusion driven by the minimization of the surface energy. In particular, we introduce the coupling between a phase-field model and the detailed calculation of the incoming material flux at the surface deposited from vacuum or vapor phase in the ballistic regime. This allows us to finely reproduce the realistic morphological evolution during the growth on nonflat substrates, also accounting for different flux distributions. A general assessment of the method, focusing on two-dimensional profiles, is provided thanks to the comparison with a sharp-interface approach for the evolution of the early stages. Then, the long-time-scale dynamics is shown in two and three dimensions, providing a general overview of the features observed during deposition on corrugated surfaces involving flattening, increasing of surface roughness with the growth of columnar structures, and voids formation.