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. Coimbrabishops, 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. Dating from this period are the remodelling (in manueline style) of the Santa Cruz Monastery, including the tombs of Kings Afonso Henriques and Sancho I, the Renaissance Manga Fountain, the altarpieces and triumphal portal of the Old Cathedral, among other works.
The University of Coimbra, was founded as a Studium Generale in Lisbon in 1290 by King Dinis I. The University was relocated to Coimbra in 1308, but in 1338 the King D. Afonso IVmake the University return to Lisbon. The University was definitively transferred to the premises of Coimbra Royal Palace in 1537 by King John III, and expanded by 1544 to occupy the Coimbra Royal Palace. Since then, city life has revolved around the state-run university. For many decades, several colleges (colégios) established by the religious orders provided an alternative to the official institution, but were gradually discontinued with the secularization of education in Portugal. Built in the 18th century, the Joanina Library (Biblioteca Joanina), aBaroque library, is other notable landmark of the ancient university. The Baroque University Tower (Torre da Universidade), from the school of the German architect Ludovice and built between 1728 and 1733, is the city’s library.
In 1772, the Marquis of Pombal, prime minister of King José I, undertook a profound reform of the university, where the study of the sciences assumed vast importance. The collections of scientific instruments and material acquired then are nowadays gathered in the Science Museum of the University of Coimbra, and constitute one of the most important historical science collections in Europe.
The first half of the 19th century was a difficult period for Coimbra, being invaded by French troops under the command of Andoche Junot and André Masséna during the Peninsular War. A force of 4,000 Portuguese militia led by Nicholas Trant dealt Masséna a heavy blow when it recaptured the city on 6 October 1810. In March 1811, the militia successfully held the place against the retreating French army. The city recovered in the second half of the 19th century with infrastructure improvements like the telegraph, gas light, the railway system, a railway bridge over the Mondego River and the renovation of the Portela bridge, in addition to the broadening of roads and expansion of the city into the Quinta de Santa Cruz.
By 1854, with the expulsion of the religious orders and municipal reforms, the need to reorganize the municipality of Coimbra forced some changes in the existing structure of the administrative divisions. Consequently, documents were sent (on 20 January 1854) to the Ministries of Ecclesiastical Affairs (Portuguese: Ministério dos Negócios Eclesiásticos) and Justice (Portuguese: Ministério de Justiça) urging the identification by the Civil Governor and Archbishop of Coimbra (Manuel Bento Rodrigues) of the number of civil parishes to preserve, their limits, the political organs to be retained, a local census and other statistics to justify the demarcation of the territory. A commission of five members, that included João Maria Baptista Callixto, António dos Santos Pereira Jardim, Roque Joaquim Fernandes Thomás, João Correia Ayres de Campos and António Egypcio Quaresma Lopes de Carvalho e Vasconcelos, were appointed to produce a plan to reduce, suppress, demarcate and establish civil parishes in the city of Coimbra and its suburbs.