The city, located on a hill by the Mondego River, was called Aeminium in Roman times. It fell under the influence, administratively, of the larger Roman villa of Conímbriga (in Condeixa-a-Nova), until the latter was sacked by the Sueves and Visigoths between 569 and 589 and abandoned. It became the seat of a diocesis, replacing Conímbriga. Although Conimbriga had been administratively important, Aeminium affirmed its position by being situated at the confluence of the north-south traffic that connected the Roman Bracara Augusta(later Braga, in the north of Portugal) and Olisipo (later Lisbon) with its waterway, which enabled connections with the interior and coast. The limestone table on which the settlement grew has a dominant position overlooking the Mondego, circled by fertile lands irrigated by its waters. Vestiges of this early history include the cryptoporticus of the former Roman forum (now part of the Museu Nacional de Machado de Castro). The move of the settlement and bishopric of Conimbriga to Aeminium resulted in the name change to Conimbriga, evolving later to Colimbria.

During the Visigothic era (around the 8th century), the County of Coimbra was instituted by King Wittiza; a sub-county of his dominion, it was established as a fief for his son Prince Ardabast (or Sisebuto), with its seat in Emínio (the Visigothic name for Coimbra), which persisted until the Muslim invasion from the south.