San Giovanni Battista (St. John the Baptist) is one of the oldest churches on Lake Como and the first church built in Varenna. Built probably before the year 1000 where an older Paleochristian building was located, its current structure is from 1151, when it was expanded.

The restoration work carried out in the 1960s brought to light the Romanic nucleus with one nave and a small apse that were hidden beneath the 17th century transformations. The original timber roof trusses were also re-discovered. An arcosolium was also found at the bottom of the façade, used as a place of entombement.

The church, built of rough grey stone without any decoration on the outside, houses important frescoes on the inside. The side walls are decorated with excellent, but poorly-preserved 14th century frescoes; the Adoration of the Three Wise Men is portrayed on the left wall and St. John the Baptist, other Saints and St. George killing the Dragon on the right. The frescoes in the apse date back to the beginning of the 16th century; the portrayal of the Redeemer between the Virgin Mary and John the Baptist, framed by a grotesque motif with the Serponti's family coat of arms is in the basin. Episodes of the Visitation and the Baptism of Christ (painted by the same artist as the others) are portrayed on the left-hand wall.

The Romanic bell tower is built in the direction of the lake, as was the habit in that time. The bells are from 1730, donated by the noble Serponti family.