Later on a Benedictine Monastery was built around the Church and on 4 February 1331 Federuccio di Guelfone was appointed as a guardian by the Abbot Ugolino di Montevibione of the Benedictine Monastery of San Pietro in Perugia and in 1339 Ser Maffeo from Perugia was appointed Rector. In fact, it was the Abbot of that Monastery who appointed the Rector and the monks who supervised the upkeep of the Church of San Clemente and the cultivation of the surrounding lands in accordance with the Benedictine motto, "Prayer and Work". Historical sources also indicate that under the initiative of the Monastery of San Pietro in Perugia a wooden bridge was built over the Tiber to connect the isolated location with the nearby settlements. In 1437 Pope Niccolò V assigned the Church to Cardinal Orsini; in 1443 Passo dell'Acqua was then transferred under the control of Prior Antonio di Francesco who in turn made it subject to the authority of Don Gigliotto di Giovanni in 1451.

On 11 April 1509 the Abbot Ignazio Manfredi of Florence suppressed the payment of taxes of Passo dell'Acqua. Those years were very turbulent in the Perugia area and in Passo dell'Acqua in particular and we unfortunately have no historical records on the following period until the beginning of 1700. The power of the Baglioni family in the Commune of Perugia diminished and, with the decreasinglevels of freedom, the economic and social conditions worsened. The saving grace was the Salt War (1540) which broke out as a result of a popular uprising against the imposition of a tax on salt by Farnese Pope, Paolo III. Perugia resisted only briefly before she was conquered by Pier Luigi Farnese, the Pope's nephew. The Baglioni palaces were destroyed (an enormous fortress was built on the ruins, the Rocca Paolina), the ancient judiciary was abolished and a Papal governor enforced. For over three centuries Perugia was under the Church's domination. This elegant structure, once completely decorated with frescoes, was used by nobles to get sunshine and to shelter themselves from the wind. There are records that indicate that in 1763 it was seen by the Bishop of Perugia, count Amadei during a pastoral visit to the nearby parish of Pieve Pagliaccia and that he praised the three exceptionally beautiful altars and the delicate and refined interior fresco paintings. In 1875 the entire property was acquired by Francesco Simonetti and his wife Stella Luporini who made it their family home. Along with their children they expanded the agricultural output and renovated the villa. The Church, which remained as a private chapel, was always open for public worship.

This elegant structure, once completely decorated with frescoes, was used by nobles to get sunshine and to shelter themselves from the wind. There are records that indicate that in 1763 it was seen by the Bishop of Perugia, count Amadei during a pastoral visit to the nearby parish of Pieve Pagliaccia and that he praised the three exceptionally beautiful altars and the delicate and refined interior fresco paintings. In 1875 the entire property was acquired by Francesco Simonetti and his wife Stella Luporini who made it their family home. Along with their children they expanded the agricultural output and renovated the villa. The Church, which remained as a private chapel, was always open for public worship. Giovanni Simonetti,the sole heir, founded in 1915 one of the first tomato preserve companies in Italy while his wife Jolanda took great care of the park and the cultivation of the mulberry-trees for silk production. The Hotel room of her name was used during the winter to give shelter from frost to the lemon trees. In 1985, one of the nephew heirs to the estate, Giancarlo Simonetti, a wood entrepreneur, (all parquet floors in the Hotel come from his Company) had the bold and ingenious idea of transforming the elegant and artistically rich villa and the surrounding buildings into a Relais (Country Inn) which he called San Clemente precisely because it was coupled with the spacious and artistically endowed Church of the same name. The Relais San Clemente was inaugurated on 25 April 1990. Today, Carlo, the Simonetti's youngest grand-nephew, welcomes the Relais guests on behalf of his Family.