Behind the high altar of the St. Pelagius' Church lies a sunken (Early) Romanesque crypt, the only of its kind in Istria, and one of only a few in Croatia. The crypt has three naves, with strong cross vaults and two small, vaulted spaces in the dead corners. In the central part, the confessio (chamber with holy tomb) is located, bearing an inscription with the name of Bishop Adam from the year 1146. During the archaeological excavations carried out in 1895, aiming to determine the foundations of the Early Christian basilica, numerous fragments of liturgical inventory from the (Early) Middle Ages were found in the crypt. Today, they are on display at the Lapidarium Museum in Novigrad.
The museum's stone collection was supplemented with further finds made during the renovation works of 1996-1999. These provided new information relevant to the dating of the origins of the crypt, the St. Pelagius' Church and the city itself. Since, typologically, the Novigrad crypt bears a likeness to that of Aquileia, it is dated to between the end of the 8th and the beginning of the 9th century.