In 1987, the renowned scholar Duccio Belgiorno discovered the rupestrian church of S. Nicolò Inferiore, a cave used as a clearing house, which three years later was acquired by the Centro Studi sulla Contea di Modica. It is considered the oldest church in Modica: it consists of a single room of about 45 square metres with an apse covered with Byzantine-style icons, where Christ Pantocrator dominates in a central position. In addition, excavation work has brought to light earthen tombs that are still largely unexplored. It is undoubtedly an eloquent and well-preserved example of rock architecture of Byzantine origin, which has left important traces not only in the Hyblean area, but throughout Sicily.
The rock church of Lower San Nicolò is located in the lower part of the town, near the bed of a stream. Its construction dates back to the time of a district that had developed outside the city walls, close to the communication routes that connected it with the coast. Due to the collapse, its articulation has been damaged, so that the original depth of the reservoir can no longer be established. It is a single-nave church with a wide apsidal semi-circle, a triumphal arch and a height difference surmounted by two steps. The presence of an iconostasis confirms that this is an Eastern cult church, probably belonging to a small nucleus of Greek origin that participated in the process of Christianisation of the settlement. In 1577, due to a shortage of income, the small church was united with the parish of St Peter. The next phase, after the 1693 earthquake, saw the construction of a new masonry church, known as San Nicolella, which today closes the rock excavation.