Under the European Union (EU) support programs, the Portuguese heritage agency carried out several actions to develop archaeological sites with adequate infrastructures to be integrated into leisure routes. The archaeological site of the Milreu Roman ruins is located in the southernmost province of Portugal—the Algarve, near the small village of Estoi. This village is in the central Algarve region, 10 km north of the city of Faro and the coastline. Archaeological excavations conducted in the late XIX-th Century, by the archaeologist Estacio da Veiga showed the existence of both a roman Villa and a temple dedicated to the cult of water. Among other constructions on this site, a medieval rural house was built some centuries ago over the existing Roman ruins. In the 1950s, the German Archaeological Institute also excavated this location discovering unique Roman artifacts and archaeological structures (mosaic floors, masonry walls, water tanks, roman baths). In the mid-1960s, the Ministry of Public Works—Historical Monuments and Buildings Division (M.O.P.—D.G.E.M.N.) carried out a safeguard program to protect the XVI-th Century Rural House by installing a reinforced concrete (RC) roof system over the existing masonry walls. Several decades after the intervention, extensive deformations occurred followed by severe wall cracking. The proposed rehabilitation strategy for this rural building used traditional building techniques to provide an adequate rehabilitation standard. The RC roof was dismantled and removed, and it was replaced by a traditional timber roof, which resulted in a large decrease in the dead load (DL) mass, and reduced the seismic risk of this historical building.