Environmentally friendly alternatives to chromium—phosphate/molybdate and cerium-modified phosphate/molybdate conversion coatings—were deposited on a carbon steel surface. Different surface analytic techniques were applied to obtain complementary information on the composition, element distribution morphology and inner structure of the coatings in order to establish the relationship between coating properties and corrosion performance. The higher protective and stronger self-healing abilities were found for phosphate/molybdate/cerium conversion coating deposited in a sulphate-containing solution. The protective barrier strength was found to be related with certain aspects of the coating morphology such like homogeneous distribution of fine crystallites and, hence, lower number of structural defects. The self-healing ability depended on both, the composition (higher amount of Ce(IV)) and micro-structural characteristics, such as defectiveness, of the conversion layer.