This study presents a procedure in which 3D electrical resistivity tomography (ERT) and ground-penetrating radar (GPR) were used to determine singularities in the foundations of protected historic towers, where space is limited due to their characteristics and location in highly populated areas. This study was carried out on the Tower of the Cathedral “Santa Iglesia Catedral de Santa María” in Murcia, Spain. The novel distribution of a continuous nonlinear profile along the outer and inner perimeters of the Tower allowed us to obtain a 3D ERT model of the subsoil, even under its load-bearing walls. This nonlinear configuration of the electrodes allowed us to reach adequate investigation depths in buildings with limited interior and exterior space for data collection without disturbing the historic structure. The ERT results were compared with GPR measurements and with information from archaeological excavations conducted in 1999 and 2009. The geometry and distribution of the cavities in the entire foundation slab of the Tower were determined, verifying the proposed procedure. This methodology allows the acquisition of a detailed understanding of the singularities of the foundations of protected historic towers in urban areas with limited space, reducing time and costs and avoiding the use of destructive techniques, with the aim of implementing a more efficient and effective strategy for the protection of other tower foundations.