A thin wire Ag/AgCl reference electrode was prepared using 50 μm Ag wire in dilute FeCl3. The wire was embedded beneath the polyurethane topcoat of two sacrificial coating systems to monitor their corrosion potential. This is the first report of a reference electrode embedded between organic coating layers to monitor substrate health. The embedded reference electrode (ERE) successfully monitored the corrosion potential of Mg primer on AA 2024-T3 for 800 days of constant immersion in dilute Harrison’s solution. Zn primer on steel had low accuracy in comparison. This is in part due to short circuiting by Zn oxidation products, which are much more conductive than Mg corrosion products. Data interpretation was improved through statistical analysis. On average, ERE corrosion potentials are 0.1 to 0.2 V and 0.2 to 0.3 V more positive than a saturated calomel electrode (SCE) in solution for AA 2024-T3 and steel coating systems, respectively. Further research may confirm that ERE obtains corrosion potential information not possible by an exterior, conventional reference electrode. The ERE is stable under polarization. AA 2024-T3 was polarized to -0.95 V vs ERE to emulate controlled potential cathodic protection (CPCP) applications. Polarizations of -0.75 V vs ERE are recommended for future experiments to minimize cathodic delamination. The ERE was utilized to analyze coating mixtures of lithium carbonate, magnesium nitrate, and Mg metal on AA2024-T3. Corrosion potential, low frequency impedance by electrochemical impedance spectroscopy (EIS), and noise resistance by electrochemical noise method (ENM) were reported. Coating performance ranking is consistent with standard electrochemical characterization and visual analyses. The results suggest anti-corrosion resistance superior to a standard Mg primer following 1600 hours of B117 salt spray. Both lithium carbonate and magnesium nitrate are necessary to achieve corrosion protection. Unique corrosion protective coatings for aluminum could be designed through continued mixture optimization. The Ag wire ERE has been utilized for the characterization and ranking of experimental coatings on metal substrates. Structural health monitoring and corrosion potential feedback of cathodic protection systems are additional uses. There is some indication that CPCP may be applied by ERE to control the substrate polarization for an organic coating system.