Co-Sn alloy coatings are electrodeposited from a choline chloride/ethylene glycol eutectic-based electrolyte, named Ethaline, containing CoCl2·6H2O and SnCl2·2H2O without any complexing agent or additive. Cyclic voltammetry shows that the co-electrodeposition of Sn and Co is feasible due to the adjacent reduction potentials of Sn(II) and Co(II) in the solution. X-ray diffraction reveals that the films mainly contain Co3Sn2 with expanded lattice parameters and pure Sn phases. Interestingly, a self-organization of layered structure with different Co content for each layer and mixed amorphous-nanocrystalline phases are formed in the electrodeposited film, which is revealed by cross-section transmission electron microscopy observations. The formation mechanism of the layered film is discussed based on the particular fluctuation of the current-time curve. The layered Co-Sn alloy coating with a total thickness of about 400 nm exhibits enhanced corrosion resistance showing a corrosion potential of −326 mV (vs. Ag/AgCl) and a corrosion current density of about 0.09 μA cm−2 in a 3.5 wt.% NaCl aqueous solution.