The aim of this study was to systematically analyze the influence of potential and the Co(II)–Ru(III) molar ratio on the electrochemical behavior of the Co–Ru system during codeposition from acidic chloride electrolytes. The equilibrium speciation of the baths was investigated spectrophotometrically and compared with theoretical calculations based on the stability constants of Co(II) and Ru(III) complexes. The codeposition of the metals was characterized using electroanalytical methods, including cyclic voltammetry, chronoamperometry, and anodic stripping linear voltammetry. The alloys obtained at different potentials were analyzed for their elemental composition (EDS, mapping), phase composition (XRD), and surface morphology (SEM). The morphology and composition of the alloys were mainly dependent on the deposition potential, which controlled the cobalt incorporation. Ruthenium–rich alloys were produced at potentials of −0.6 V and −0.7 V (vs. SCE). In these conditions, cobalt anomalously codeposited due to the formation of the CoOH+ intermediate, triggered by the intense hydrogen evolution on the ruthenium sublayer. Bulk cobalt electrodeposition began at a potential of around −0.8 V, resulting in the formation of cobalt-rich alloys. The early stages of the electrodeposition were investigated using different nucleation models. A transition from 2D progressive nucleation to 3D instantaneous nucleation at around −0.8 V was identified as being caused by cobalt incorporation. This was well correlated with electroanalytical data, partial polarization curves of alloy deposition, elemental mapping analysis, and the structure of the deposits.