The role of the amorphous carbon layer on phosphate formation is investigated in multi-phase steel. To investigate site-specific characterization for the remained organic contaminants which possess C-C/C-H species, the amorphous hydrogenated carbon (a-C:H) which possesses both C-C bond and C-H bond is deposited on the steel surface using the electron beam-induced deposition method. As the amorphous carbon film introduces, the main factor determining the dissolution rate in the multi-phase steel is changed from carbon contents on the surface to external amorphous carbon film when no external oxides exist. Despite the high electrical transportation of sp2-bonded carbon, the carbon layer acts as an effective physical barrier due to the amorphous structure, resulting in the phosphate-uncovered surface. The detailed microstructure analysis clarifies the inhibition mechanism of the phosphate formation on the carbon-deposited steel surface.