In the framework of the EU–UNDP project ‘Rehabilitation of Old Nicosia’ (Cyprus, 2004–9), a high-resolution geoelectrical survey has been performed inside the partially ruined monumental complex of St Nicholas of the English, now called the Bedestan, which was designed to become a venue space for cultural activities. The aim was to detect buried traces of a Byzantine basilica of the sixth century, on the ruins of which, according to tradition, the construction of St Nicholas was begun in the 12th century. The survey has been conducted on the floor of the monument, using a dipole–dipole electrode array along two perpendicular sets of profiles. In order to model the resistivity distribution, the probability-based electrical resistivity tomography inversion (PERTI) method has been applied. Sets of aligned blocks with resistivity in the range 100–400 ohm·m, bounding a three-room rectangular space, and traces of a rounded structure with mean resistivity about 150 ohm·m, appearing at one extremity of the central room, are the main resistive features recognized down to 4 m depth, within a conductive background with resistivity in the range 20–40 ohm·m. Altogether, these resistive features, showing in plan the shape of a church characterized by a central nave with an apse and two side aisles, have been interpreted as an evidence of the existence of remains of the earlier Byzantine basilica. Moreover, small volumes with resistivity in the range 10–12.6 ohm·m have been found, scattered underneath the whole surveyed area. Taking into account the PERTI results, ground-truth has been performed in two sites, designed to become two permanent protected exposures of the archaeological findings beneath the floor of the newly restored Bedestan. At one site, excavations detected remains of masonry in correspondence of the alignment of resistive blocks at the left margin of the left side aisle of the churchlike structure. At the other site, graves, entirely filled with wet debris in an alluvial soil matrix, have, instead, been found in correspondence with the greatest conductive volume, detected outside the perimeter of the churchlike structure. Both findings have been dated back to the sixth century. Since the Bedestan case-history is one of the first applications of the PERTI algorithm to real field data sets, its performance has been tested using the well-known ERTLabTM commercial software as benchmark. The comparison has shown a general consistency between the two inversions, and also confirmed the much higher computing speed, better filtering capacity and greater versatility of the PERTI algorithm, already outlined in a previous paper where only synthetic models were tested.