EN AW-6016-T4 aluminum alloy sheets were joined with zinc-coated DC04 steel sheets using the Cold Metal Transfer (CMT) welding process. Si-rich and virtually Si-free commercial filler alloys Al-3Si-1Mn (AA-4020) and Al-4.5Mg-Mn-Zr (AA-5087) were used. The influence of silicon on the formation and morphology of intermetallic phases in the joints was studied. The intermetallic seam was investigated by scanning electron microscopy (SEM), electron microprobe microanalyzer (EPMA) using wavelength dispersive spectroscopy (WDS), and transmission electron microscopy (TEM) using selected area electron diffraction (SAED), energy dispersive spectroscopy (EDS), and electron energy loss spectroscopy (EELS). Short-range ordered (SRO) η-Al₅Fe₂, long-range ordered (LRO) η'''-Al₅Fe₂, and θ-Al₁₃Fe₄ phases formed in the Si-poor and Si-rich welds. The presence of Si in the filler metal leads to the additional formation of the α_c-Al(Fe,Mn)Si phase. Grains containing η and η''' were identified. The continuous η seam was generally thinner for higher Si contents. It was found that Si contents higher than 3-3.5 at% in the η seam suppressed the formation of LRO η''' and favored the formation of η.