This paper proposes an innovative approach in characterization of silicon-based chromium (VI) replacement coatings on an Al substrate by using, salt spray tests and time-of-flight secondary ion mass spectrometry (ToF-SIMS) performed in profile mode by a gas cluster ion beam source (GCIB). While salt spray tests highlight the difference in anticorrosion behaviour, ToF-SIMS provides molecular information on the entire coating and even down to the interface with the Al substrate. ToF-SIMS revealed Si2O2+ and SiOAl + fragments which both contribute to understanding the differences in the anticorrosion performance which are found in the salt spray tests. Si2O2+ moieties relate to the cross-linking density of the coating and subsequently determines the barrier properties. SiOAl+ originates from the interface and characterizes the actual “conversion” of Al at the interface by the deposited layer. The differences in the profile of Si2O2+ and SiOAl + explained the respective anticorrosion performance. From the tested coatings PCT161 showed the highest intensity for both Si2O2+ and SiOAl + while simultaneously performing the best results in the salt spray test. These observations highlight that Si2O2+ and SiOAl + fragments are good indicators of anticorrosion performance and are confirmed by salt spray tests. Moreover, PCT161 and PCT146 are true conversion coatings capable of replacing chromium-based systems.