The microstructure of electrodeposited Au-Ni films was investigated by means of X-ray diffraction (XRD), transmission electron microscopy (TEM), and scanning transmission electron microscopy (STEM). Nano-crystalline films were found to be composed of three different phases: Au-rich crystalline phase, Ni-rich crystalline phase, and Ni-rich amorphous phase. Particles of carbon measuring 5 to 20 nm were also found in the deposit. It is assumed that the inclusion of a large amount of carbon particles causes the formation of the amorphous phase. The microstructure and the state of dispersion of the carbon particles were also investigated. The results of TEM and STEM observations showed that the carbon particles possess either the graphite structure or the amorphous structure with some of the particles being arranged in arrays. Scanning tunneling microscopy (STM) was performed to study the relationship between the structure of species adsorbed on the electrode surface and the process of carbon inclusion.