Achieving historically anticipated improvement in the performance of integrated circuits is challenging, due to the increasing cost and complexity of the required technologies with each new generation. To overcome this limitation, the exploration and development of novel interconnect materials and processes are highly desirable in the microelectronics field. Molybdenum (Mo) is attracting attention as an advanced interconnect material due to its small resistivity size effect and high cohesive energy; however, effective processing methods for such materials have not been widely investigated. Here, we investigate the electrochemical behavior of ions in the confined nanopores that affect the electrical properties and microstructures of nanoscale Mo and Mo–Co alloys prepared via template-assisted electrodeposition. Additives in an electrolyte allow the deposition of extremely pure metal materials, due to their interaction with metal ions and nanopores. In this study, boric acid and tetrabutylammonium bisulfate (TBA) were added to an acetate bath to inhibit the hydrogen evolution reaction. TBA accelerated the reduction of Mo at the surface by inducing surface conduction on the nanopores. Metallic Mo nanowires with a 130 nm diameter synthesized through high-aspect-ratio nanopore engineering exhibited a resistivity of (63.0 ± 17.9) μΩ·cm. We also evaluated the resistivities of Mo–Co alloy nanowires at various compositions toward replacing irreducible conventional barrier/liner layers. An intermetallic compound formed at an Mo composition of 28.6 at%, the resistivity of the Mo–Co nanowire was (58.0 ± 10.6) μΩ·cm, indicating its superior electrical and adhesive properties in comparison with those of conventional barriers such as TaN and TiN. Furthermore, density functional theory and non-equilibrium Green’s function calculations confirmed that the vertical resistance of the via structure constructed from Mo-based materials was 21% lower than that of a conventional Cu/Ta/TaN structure.