This work is focused on creating coating layers made of a metakaolin-based geopolymer suspensions (GP)-formed Al matrix modified using H3PO4 acid with Al(OH)3 in isopropyl alcohol, named GP suspension I, and H3PO4 acid with nano Al2O3 in isopropyl alcohol, named GP suspension J. The selected GP suspensions were applied on aluminum and steel underlying substrates as single-layer coatings and multi-layer coatings, where multi-layer coatings included three and five layers that were polymerized by a curing process. Curing was divided into two types with every layer curing process and final layer curing process. For both GP suspensions I and J, the effect of the number of layers and the type of substrate on adhesion was investigated. The prepared samples on underlying substrates were characterized on the microscopy analysis including SEM for high-resolution images and 3D laser confocal microscopy (CLSM) for the 3D visualization of the coatings structure. Microscopy analysis showed structural defects such as porosity, cracks and peeling, which increase with a greater number of applied layers. However, these defects were only evident on a micro scale and did not seem to be fatal for the performance of the surface stability. The EDS mapping of the prepared layer showed inhomogeneity in the distribution of elements caused by the brush application. A grid test and thickness measurement were performed to complete the microscopy analysis. The grid test confirmed a very high adhesion of GP coatings on the aluminum substrate with a rating of one (only in one case was there a rating of two) and a lower adhesion on the steel substrate with the most frequent rating of three (in one case, there were ratings of two and one). The thickness measurement proved a noticeably thicker thickness of the prepared layer on the Fe substrate compared to the Al substrate by 20%–30% in the case of suspension I and by 70%–10% in the case of suspension J. The thickness of the layer also showed a dependence on the method of application and curing, as a thicker layer was always achieved when curing after the final layer of the GP suspension, compared to curing after each applied layer. The resulting single-layer and multi-layer thicknesses ranged from approx. 7 to 30 µm for suspension I and from approx. 3 to 11 µm for suspension J. A non-linear increase in thickness was also evident from the thickness measurement data.