The church of Saint John is situated 1 km west of Shën Jan village on the eastern part of a small hilltop, known locally as Shijan, left of Kalasa River. The first excavation season took place in 2001 and was intended to reveal the monument’s outline. Ten trenches were excavated: three in the central nave, two in the narthex, two in the lateral naves and the last one in the frontal part of the church. This excavation season revealed the existence of two lateral naves and two apses.

The second archaeological season at Saint John’s church was undertaken in 2002 and brought to light other undiscovered parts of the monuments. The central nave is 14.35 – 14.50 m long and 4.75 – 4.95 m wide, while the chord of the apse is 2.85 m and its depth 3.75 m. The narthex is 11.50 m wide and 3.95 m long. The lateral naves are approximately of the same length while they differ in width: the south nave is 11.50 m wide and the northern nave is 2.50 m. The naves are separated by blind arcades resting above engaged piers. Each of the arcades has three arches, while another arch crowns the entrance into the sanctuary area. During the excavation of the southern nave a monumental doorway with two antes was discovered. In a second phase these were created by the alteration of the engaged piers and columns of the doorway. This doorway in a second phase was reduced in size from 1.30 m to 0.70 m. During this season two graves were also excavated in the central nave. One of them was inside the nave floor and the other, better preserved, is in one of the ambon basements.

The archaeological season of 2003, discovered a three nave basilica, with arches, three apses on the east side and a narthex on the west side. The central apse is a three-sided structure on the outside and its interior is of semicircle shape. The northern apse is semicircular, whereas the shape of the southern apse was not determined during this excavation season. The excavation revealed four entrances with porches: one on the west and the other on the north of the narthex, while the two others were on the north side, approximately in the middle of the lateral aisles. A large quantity of frescos fragments was also found. The construction materials yielded by the excavations consist mainly of stones, bricks and tiles. The latter are of different types and sizes and some of them bear monograms.