In order to confirm and reinforce the power of the concelho (municipality) he conceded a formal foral (charter) in 1179.
Already in the Middle Ages, Coimbra was divided into an upper city (Cidade Alta or Almedina), where the aristocracy and the clergy lived, and the merchant, artisan and labour centres in the lower city (Arrabalde or Cidade Baixa) by the Mondego River, in addition to the old and new Jewish quarters.
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) 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.
Henry expanded the frontiers of the County, confronting the Moorish forces, and upon his death (in 1112), Theresa, Countess of Portucale and Coimbra, unified her possessions.
It stood too close to the river, and frequent floods forced the nuns to abandon it in the 17th century, when the Monastery of Santa Clara-a-Nova was built uphill.
In the 15th and 16th centuries, during the Age of Discovery, Coimbra was again one of the main artistic centres of Portugal thanks to both local and royal patronage.
Coimbra bishops, religious orders and King Manuel I supported artists like Diogo Pires (father and son), Marcos Pires, João de Castilho, Diogo de Castilho and the Frenchmen, João de Ruão and Nicholas of Chanterene, among others, who left important Manueline and Renaissance works in the town.
Although it was not a large settlement, Qulumriyah (Arabic: ), in the context of Al-Andalus, was the largest agglomerated centre along the northern Tagus valley, and its principal city boasted a walled enclosure of 10 hectares, supporting between 30 inhabitants.
Remnants of this period include the beginnings of the Almedina, Arrabalde and the fortified palace used by the city's governor (which was later converted into the Royal Palace by the early Portuguese monarchs).