Cost efficiency and sustainability are critical challenges for future accelerator machines. Nb-coated Cu (Nb/Cu) superconducting radiofrequency (SRF) accelerating cavities, while requiring R&D to meet high acceleration gradient performance standards, show potential for addressing these challenges. Defects in the Nb layer responsible for the deterioration of cavity performance have been linked to the underlying Cu substrate. This study investigates a novel optimization method by mitigating the substrate surface’s impact on deposited Nb, using High Power Impulse Magnetron Sputtering alongside a DC substrate bias (from −50 to −300 V). Trenched silicon substrates are chosen to emulate substrates with exceptionally rugged surface characteristics. Film deposition is investigated both experimentally and through kinetic Monte Carlo simulations. Higher DC voltages are shown to eliminate self-shadowing during the coating process via improved incident ionic flux directionality, enhanced adatom mobility and increased re-sputtering rates, ultimately yielding flat and densely-packed films. The influence of the substrate’s shape on the film’s surface was found to decrease exponentially with increasing ion bombardment energies. Films sputtered under high DC bias conditions (−300 V) exhibited complete planarization with a 30% re-sputtering rate. Strategies for applying this technique to Nb/Cu SRF cavities, enhancing their viability for future particle accelerators, are also discussed. •Simulation and Nb thin film deposition by HiPIMS at different ion bombardment energies.•Film planarization on trenched Si substrates achieved with high ion bombardment energies.•Experimental confirmation of simulated planarization effect by ion bombardment.•Elimination of the influence of the substrate’s surface morphology on films deposited at higher energies.•Potential mitigation of Q-slope phenomenon on Nb/Cu SRF cavities and improved energy efficiency of accelerators.