People have lived in this area since the Neolithic period, but it has been continuously inhabited since the conquest by Roman legions, who established an outpost and took over the existing castros in the area. It developed into a military centre known for its baths. The Romans built defensive walls, spanned the river with a bridge, and exploited the local mines. The importance of the town led to it being elevated to the status of a city in 79 AD, during the reign of the first Flavian Caesar, which was also reflected in its name, Aquae Flaviae.

Rome's hegemony lasted until the 3rd century, when, successively, the Suebi and Visigoths as well as the Alani colonized the settlements of Chaves. The area surrendered to Islamic forces at around 714-716. The city was conquered by Alfonso I of Asturias in 773 and repopulated in 868 by Alfonso III of Asturias. Battles between Christian and Muslim forces then continued until the 11th century, when Alfonso V of León permanently reconquered Coimbra, establishing a firm buffer-zone to the south. He reconstructed, settled and encircled the settlement of Chaves with walls, in addition to establishing a Jewish quarter in the community. It was in the reign of Afonso I of Portugal that it was taken from León and firmly integrated into the Kingdom of Portugal domain (1160). Owing to its geographic location King Denis, ordered the construction of a castle to protect the kingdom's border.

The Ponte de Trajano, was built at the end of the 1st century. Approximately 150 meters long and with a dozen visible arches it became a pedestrian bridge in 2008