The regular application of geophysical survey techniques to evaluate archaeological sites is well established as a method for locating, defining, and mapping buried archaeological materials. However, it is not always feasible to apply a range of different methods over a particular site or landscape due to constraints in time or funding. This paper addresses the integrated application of three geophysical survey methods over an important archaeological site located in south Italy. In particular, it is focused on the results achieved from a past geophysical survey and the ongoing excavations performed by archaeologists in the site of Muro Leccese. Muro Leccese (Lecce) is one of the most important Messapian archaeological sites in southern Italy. The archaeological interest of the site was generated since the discovery of the remains of Messapian walls (late 4th–3rd centuries BC). With the aim of widening the archaeological knowledge of the Messapian settlement, several integrated methods, including magnetometry, ground-penetrating radar, and electrical resistivity tomography were used on site to fulfill a number of different research objectives. Since the most important targets were expected to be located at shallow soil depth, a three-dimensional (3D) ground-penetrating radar (GPR) survey was carried out in two zones, which were labeled respectively as zone 1 and zone 2, and were both quite close to the archaeological excavations. The GPR investigations were integrated with a 3D electrical resistivity tomography (ERT) survey in zone 1 and with a magnetometric, in gradiometry configuration survey in zone 2. The integration of several techniques allowed mapping the structural remains of this area and leading the excavation project. The geophysical results show a good correspondence with the archaeological features that were found after the excavation. Current work on the geophysical survey data using different codes for the processing of the data and merging different datasets using a Geographic Information System allowed achieving a user-friendly visualization that was presented to the archaeologists.