The present study investigates the surface and in-depth characteristics, and deposition mechanism of zirconium-based conversion coatings on hot dip galvanized (HDG) steel substrates for automotive applications, based on zinc galvanizing baths with small additions of aluminium. This contribution provides scientific proof of the chemical heterogeneity both at the surface and along the depth of the Zr-based conversion coatings on galvanized steel. To this purpose, the definition of two derivative model systems – pure zinc and pure aluminium – was indispensable due to Al-enrichment phenomena observed at the galvanized steel surface. A 3D evaluation of the sample chemistry before and after formation of the Zr-based conversion coatings was conducted by a combined approach based on X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) with 1-keV Cs+ sputtering. The experimental results provide direct evidence of the fact that Zr-based conversion coatings on the HDG steel are constituted by a mixed Zn, Al and Zr oxyhydroxide in combination with Zr oxy-/hydroxyfluoride on top of a complex fluoride (hydr)oxide Zn/Al layer, rather than a pure ZrO2 film on top of the galvanized layer mainly made of zinc (and aluminium) as previously reported in the literature.