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The adsorption of organic ionic dyes on different pore size engineered silica materials with potential application for industrial wastewater treatment has been investigated using Fourier transform laser microprobe mass spectrometry (FT-LMMS) and time-of-flight secondary ion mass spectrometry (TOF-S-SIMS). The complementary use of the two methods with different information depth allowed data on the subsurface distribution and pore penetration of the adsorbed organic compounds. Macroscopic methods were employed to determine the amount adsorbed on the particles and the specific external surface area. Local MS analysis allows identification of the organic dyes exclusively at the outer particle surface when the pore size is inferior to the size of the adsorbing molecule, or at the surface of the channels inside the material. Specifically, the monolayer information depth of TOF-S-SIMS causes a signal to refer essentially to the adsorbate at the outer particle surface, which is only a fraction of the total adsorption in mesoporous materials, while FT-LMMS allowed detection of the presence of adsorbates at the outer surface as well as inside the subsurface of 10 to 50 nm depending on the material under study. The observed data open perspectives for the molecular monitoring of the adsorption behaviour of different materials at the (sub) microm scale.