In Roman times, the area was devoted to vacationing and relaxation, with many private villas dotting the landscape. The nearby town of Venta de Baños is presently larger and more important than Baños de Cerrato.
The church was commissioned by the Visigothic king Reccesuinth of Hispania (the Iberian Peninsula, comprising modern Spain and Portugal), in the year 661 and whose solemn consecration ceremony is believed to have taken place on the 3rd of January, 661. It is located in a the fertile Pisuerga River valley, near the confluence with the Carrión River. In Roman times as under the Visigoths, this was an important grain-producing region.
History explains why the Visigothic king ordered the construction of this church:
The Gothic King Reccesuinth was returning from a victory over the leader of the Basques, Fruela, and in this little town he took a rest from his journey, as he had a kidney disease. While he was resting here he drank water from a spring that was in a place where there had once been Roman baths and he suddenly recovered from his illness. He attributed this to a miracle. In thanks, he decided to erect a church in that place, which is the one that we still see there, dedicated to St. John the Baptist.
The church was built as a royal foundation under the control of the Bishops of Palencia. According to scholars, it is the oldest and most original extant Visigothic church in Spain. Moreover, it has an original inscription in the stones over its triumphal entry, in awkward capital letters. This text is also preserved in a codex of the Tenth century, copied from a Toledan manuscript from the Eighth century.
The excavations that were carried out in 1956 and 1963 yielded a medieval necropolis of 58 tombs to the north-west of the church and discovered three pieces of Seventh century bronze: two belt buckles in the shape of a lyre and one liturgical object.