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The small church is located right in the medieval part of Viterbo and owes its name to the ancient custom of digging defensive ditches that were called charcoal pits or carbonare.

The construction dates back to the 12th century and was the seat of the Knights Templar, the most famous Christian religious knightly order. It was born in the Holy Land during the First Crusade to defend pilgrims and the Holy Places (Templar comes from the Temple of Jerusalem) and became a monastic order in 1129 with Bernardo di Chiaravalle. The knights therefore had a double role as a soldier-monk and over time they entered every aspect of western social and religious life until the king of France suspended the order in 1312.

The church was then entrusted to the Knights of Rhodes, who settled for a few years in Viterbo after the conquest of the Turks.

The church today appears with a very modest and simple aspect. The ancient painting of the Madonna della Carbonara is today in the Museo del Colle del Duomo.