The electrodeposition of cobalt nanowires into nanoporous alumina templates produced by one-step anodization of low-purity aluminium was investigated. Aluminium was electropolished prior anodization to generate a hexagonal cell pattern, and a tree-like structure was introduced at the aluminium/aluminium oxide interface by progressively decreasing the anodization potential following potentiostatic anodization. Pulsed electrodeposition including the periodic application of a cathodic potential pulse with constant amplitude was performed to fill the generated alumina template by cobalt nanowires. With this strategy, cathodic potential pulses with amplitude lower than −5 V (vs. Ag/AgCl) were necessary to enforce uniform and instantaneous cobalt nucleation at the bottom of template nanopores, which allowed achieving uniform filling and narrow length distribution of the electrodeposited nanowires. However, the uniform growth of the nucleating cobalt nanowires could be sustained by considerably less cathodic potential pulses (up to −1.5 V vs. Ag/AgCl). Uniform filling of the alumina template could accordingly be achieved by a two-stage-pulsed electrodeposition strategy including the application of a high cathodic pulse (<−5 V) inducing uniform and instantaneous cobalt nucleation followed by the periodic application of a lower cathodic pulse (>−1.5 V) sustaining nanowire growth. The mechanisms that govern cobalt nucleation at the bottom of nanopores and the technical advantages of the proposed nanowire synthesis strategy are discussed.