Micrometer-thick cobalt-indium (Co-In) films consisting of self-assembled layers parallel to the cathode plane, and with a periodicity of 175 ± 25 nm, were fabricated by electrodeposition at a constant current density. These films, which exhibit spatio-temporal patterns on the surface, grow following a layer-by-layer mode. Films cross-sections were characterized by electron microscopies and electron energy loss spectroscopy. Results indicate the spontaneous formation of nanolayers that span the whole deposit thickness. A columnar structure was revealed inside each individual nanolayer which, in turn, was composed of well-distinguished In- and Co-rich regions. Due to the dissimilar magnetic character of these regions, a periodic magnetic nanopatterning was observed in the cross-sectioned films, as shown by magnetic force microscopy studies.