The building currently known as the Royal Palace was built at the end of the 10th century, serving as a fortress for the governor of the city during Islamic rule. In 1131, it became the first Portuguese royal household, the residence of Afonso Henriques, the first king of Portugal. In 1537, during the reign of King John III, the University was permanently relocated from Lisbon to Coimbra, having been established in this building in 1544.

This building is divided into 3 spaces:

The Armory

This room is thus named because it was the first line of defence in the protection of the Princes, given their importance in the line of succession to the throne. Later, this space was also used to store the weapons of the old Academic Royal Guard. Today, they are used by the Archers (guards) during solemn academic ceremonies, such as the awarding of Honoris Causa doctoral degrees, the swearing in of the Rector and the solemn opening of the academic year. The Academic Royal Guard was the guard corps that ensured the security of the rector, the rector's house, the university buildings and the urban boundaries that fell within the jurisdiction of the University. The guards were originally known as Verdeais. After 1836, they became known as archers, even though they never used crossbows. They donned a kind of military uniform for daily use. Their current uniform dates back to the second half of the 20th century.

The walls of the Yellow Room, adjacent to the Armory, are lined with yellow silk in honour of the Faculty of Medicine, because this is where the "Congregation of the Faculty of Medicine" would meet. This space was a meeting room where members of the Faculty would discuss a wide variety of issues. The other rooms, each with a different colour, represent the other faculties. The rooms are still used today for academic activities.

The portraits of the University rectors who served in the 19th and 20th centuries can still be seen.

The Great Hall of Acts

This hall is the most important space at the University of Coimbra. It was the old Throne Room, and was the residence of the kings of the first Portuguese dynasty between 1143 and 1383. Important events in the history of portugal took place here, such as the proclamation of King John I in 1385.After the University opened in the Palace of Schools, this space became the main hall of the University of Coimbra, where the most important ceremonies of the academic life took place.

The current design of this hall is the result of renovations carried out in the mid-17th century. The walls were lined with "carpet-like" tiles manufactured in Lisbon. The wooden ceiling was renovated with 172 panels that look like grotesque motifs (representing sea monsters, Indians, mermaids, plants).

The walls are lined with the portraits of all of the Portuguese kings - from King Afonso Henriques to King Manuel II - with the exception of the Phillipine dynasty (from 1580 to 1640).

The new monarch, King John IV, offered the Crown of Portugal to Our Lady of the Immaculate Conception in thanksgiving, proclaiming her the patroness of the Kingdom. This required the support of the lentes (lecturers) of Coimbra who, headed by the Rector, took a solemn oath to Our Lady in 1646, which was recorded on stone plaque in St. Michael's Chapel. Since then, Portuguese monarchs ceased to wear a crown.

Private Examination Room

During its existence as the royal palace, this space served as the king's quarters, but was later transformed into a venue where the graduates take their examinations. The examination consisted of an oral test taken at dusk. It was a private event, that is, only the student to be assessed and the professors could be in the room.

This examination continued up until the second half of the 18th century, having been abolished during the reforms carried out by the Marquis of Pombal during the reign of King Joseph I.

These reforms revolutionised education in Portugal, having a deep impact on the University of Coimbra, with the introduction of the ideas and values of the Enlightenment. The first great change was the expulsion of the Jesuits from the country. This was followed by the great reform to the University, which in particular saw the introduction of new areas of study such as Physics, Chemistry, Biology, Astronomy.

To achieve this, the Marquis carried out a series of architectural works that transformed the University spaces: the Botanical Garden and Astronomical Observatory, which were built in the Palace of Schools, but were demolished during the 1950s. In addition to this, the buildings left empty by the Society of Jesus were renovated: the Chemistry Laboratory (former Jesuit dining hall) and the College of Jesus, the order's former province house, where the Physics Office and the Natural History Gallery were built. Today, these spaces make up the Science Museum of the University of Coimbra.

The ceiling in this room dates back to 1701. One can see the coat of arms of the Kingdom of Portugal and representations of the former great Faculties at the University of Coimbra: Theology (Cross and Sun), Law (Scale and Sword), Medicine (Swan and the Staff of Hermes) and Canon Law (Papal Mitre).

The walls of the room contain portraits of the 38 rectors from the 16th to the 18th centuries, together with the length of their terms: the caption records the number of days, months, and years that the rector headed the University. Today, the Rector's term of office is limited to a maximum of 8 years (two 4-year terms).