Oxide and nitride thin-films of Ti, Hf, and Si serve numerous applications owing to the diverse range of their material properties. It is therefore imperative to have proper control over these properties during materials processing. Ion-surface interactions during plasma processing techniques can influence the properties of a growing film. In this work, we investigated the effects of controlling ion characteristics (energy, dose) on the properties of the aforementioned materials during plasma-enhanced atomic layer deposition (PEALD) on planar and 3D substrate topographies. We used a 200 mm remote PEALD system equipped with substrate biasing to control the energy and dose of ions by varying the magnitude and duration of the applied bias, respectively, during plasma exposure. Implementing substrate biasing in these forms enhanced PEALD process capability by providing two additional parameters for tuning a wide range of material properties. Below the regimes of ion-induced degradation, enhancing ion energies with substrate biasing during PEALD increased the refractive index and mass density of TiOx and HfOx and enabled control over their crystalline properties. PEALD of these oxides with substrate biasing at 150 °C led to the formation of crystalline material at the low temperature, which would otherwise yield amorphous films for deposition without biasing. Enhanced ion energies drastically reduced the resistivity of conductive TiNx and HfNx films. Furthermore, biasing during PEALD enabled the residual stress of these materials to be altered from tensile to compressive. The properties of SiOx were slightly improved whereas those of SiNx were degraded as a function of substrate biasing. PEALD on 3D trench nanostructures with biasing induced differing film properties at different regions of the 3D substrate. On the basis of the results presented herein, prospects afforded by the implementation of this technique during PEALD, such as enabling new routes for topographically selective deposition on 3D substrates, are discussed.