The origin of poor phosphatability in multi-phase steel is studied by various microscopic methods. The effect of the three influential factors that are a phase including compositional difference, crystallographic orientation, and surface oxidation on the zinc phosphate (ZP) formation are investigated by the comparative study of the matrices under the ZP-formed and -missing areas. The inferior ZP formation in bainite/martensite than ferrite is clarified by the analyses of a transmission electron microscopy and an electron backscatter diffraction. The matrix orientation doesn't show apparent deference in the ZP-formed and -missing matrices. The ZP-missing area shows only the enrichment of carbon in the analyses of an electron probe microanalyzer, an Auger electron spectroscopy, and a secondary ion mass spectrometry. The alloy showed no oxide film at the ZP-missing area due to the pickling process. The poor phosphatability in the multi-phase steel is further discussed on the relatively lower matrix dissolution rate at the carbon-rich bainite/martensite area in the ZP solution.