The Visigoth king Flavius Recesvinto founded the Monastery of St. John the Baptist on January 3, 661, of which only the church we now comment on remains.
This church has suffered numerous reconstructions throughout its history, in spite of the compact volumes, the irregular rigging, the narrow loopholes with spillage opened in the high part of the wall of the arcade that rises in the central nave, give faith of the antiquity of this Visigothic construction that, in spite of the reconstructions, has not had more attachment than the Spanish bell tower. It is therefore considered to be the most original and Spanish church of all Visigothic medieval art.
The king Recesvinto to the return of his fights with the vascones and sick of a renal affection, stopped in these thermal baths (source of medicinal waters) and as he felt a great improvement he decided to construct a basilica dedicated to San Juan Bautista in thanksgiving.
In the 8th century, during the Muslim domination, Baños de Cerrato was partially depopulated, and the basilica was partially destroyed. From the 9th century it was repopulated again and in the 12th century the basilica belonged to the heritage of Queen Doña Urraca. Later it belonged to the monks of San Isidro de Dueñas and later it was a parish church until the 16th century to become a hermitage in the 17th century.
Despite the Muslim invasion, the basilica of San Juan did not suffer excessive damage by Muslims, due in part to the great respect that the figure of St. John the Baptist inspires Islam.