The archaeological zone of Mitla has an invaluable place within the Mexican cultural heritage. This pre‐Hispanic city concentrated the political and religious power of the central valleys of Oaxaca, south of Mexico, mainly during the Postclassic period. However, despite its great cultural importance and considering the risk to its monuments due to the high seismicity of the region, very few studies have focused on the systematic exploration of the subsoil of this area. The present research aimed to characterize the subsoil of one of the architectural compounds of the archaeological zone, the Group of the Columns, aiming to identify possible underground elements such as architectural structures, tunnels or tombs. For that purpose, three non‐invasive geophysical methods were applied, ground penetrating radar (GPR), electrical resistivity tomography (ERT) and ambient noise tomography (ANT). In the palace, all three methods showed the presence of a substructure below the Hall of the Columns. In the Plaza of the Columns, the GPR detected anthropogenic walls and platforms at different depths that suggest a different configuration of the square and a more prolonged occupation of this group. The results open the discussion about the temporality of the first construction of this architectural group.