Mg and its alloys are highly prone to corrosion, which is an important consideration in many industries and applications. However, most available methods for studying the buildup of Mg corrosion layers as a function of time—an indirect measure of corrosion rate—are not sufficiently sensitive to monitor the early stages of the process. In this letter, a simple and innovative method is reported for monitoring changes in Mg corrosion layer thickness in various solutions, under close-to-natural conditions and starting from the first minutes of the process. Dip-pen nanolithography (DPN) was first used to pattern poly(methyl methacrylate) (PMMA) reference lines on the surface of the Mg alloy AE53, so as to indicate the initial conditions. Then, AFM was used—for the first time to the best of our knowledge—to measure the thickness of corrosion layers forming on three adjacent 100 µm × 100 µm surface areas at several time points (5–30 min) after immersion in solution. Test solutions included either saline or phosphate-buffered saline (PBS), in each case either with or without the addition of Fenton reagents, which are known to accelerate corrosion and are highly relevant for biological implants that employ Mg alloys as degradable substrates. In all tested solutions, the buildup of corrosion layers showed the expected dynamics—namely, an increase followed by a decrease and again an increase in layer thickness; however, the layers were considerably thicker in PBS than in saline, and in solutions with Fenton reagents than in those without them. These results demonstrate the unique advantage of the AFM instrument, as compared with other methods (such as SEM and potentiodynamic polarization), for measuring corrosion buildup, as the layer growth process can be accurately measured under natural conditions, in the presence of solutions, and from its very early stages. We report a simple and an innovative method for monitoring changes in corrosion layer thickness in various solutions, under close-to-natural conditions, starting from the first minutes of the process. We used dip-pen nanolithography by the NLP2000 to pattern reference lines on the surface of the Mg alloy AE53, which allowed us to accurately monitor the buildup of the corrosion layers using AFM at various time points after immersion in saline and PBS with or without the addition of Fenton reagents.