The patron saint of San Giovanni Lupatoto is Saint John the Baptist, celebrated on 24 June in the church named after him.
The municipal territory also holds the Sanctuary of the Madonna dello Staffalo, also known as the Sanctuary of the Madonna dello Staffalo of the Moors or of the Germans, and the church of the hamlet of Sorio. The town takes part of its name from its patron, while the epithet «Lupatoto» recalls the ancient origins linked to the presence of wolves in the surrounding marshland.
