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In this work, three-dimensional Electrical Resistivity Topographies are applied to an ancient monument to investigate its foundations. In this framework, we propose and test special measuring strategies based on optimized 3D measuring protocols that depict the foundations of building structures with electrodes located at both sides of the targeted area. The different 3D electrode layouts and protocols were tested extensively with synthetic data against more standard electrode configurations. In addition, the methodology was tested in real field conditions at parts of the Thessaloniki’s Byzantine Wall. Inversion results from the three-dimensional ERTs prove the proposed scheme’s ability to delineate the foundations’ depth while requiring a minimum footprint on the monument.