The building of St. Michael's Chapel was probably built in the 12th century and served as the private oratory for the former Royal Palace. It is named after Archangel Michael, the protector of King Afonso Henriques (first king of Portugal).

On the outside, the large portal dominates the façade. This naturalistic structure is flanked by two pillars covered in strong maritime symbolism. At the centre is the Portuguese Royal Crest, together with the Cross of Christ and the Armillary Sphere The current structure is the result of restoration to the Royal Palace, carried out during the 16th century on the orders of King Manuel. Inside the Chapel we find various decorative motifs with a distinctive religious theme. The current decor is the result of work carried out mainly in the 17th and 18th centuries. The highlights of this space, which is both sumptuous and harmonious, are the ceilings, the traditional tiled walls, the high altar, the Tabernacle and the organ.

The large altar-piece, which covers the wall above the high altar with a large central throne, dates back to the 18th century and is decorated with golden gilt. To the left is a representation of Archangel Michael. In addition to the high altar, there are two other side altars; to the left is the altar of Our Lady of Light, the patronness of the academic community, and two smaller statues representing St. Joseph and St. Augustine; to the right is the altar of St. Catherine and the statues of Jesuits Ignatius of Loyola and Francis Borgia. Next to this altar is a statue of the Immaculate Conception, the patroness of the University and of Portugal.The white and blue patterned tiles lining the high altar were laid in 1613. The tiled walls, forming a kind of "carpet", that cover a large part of the chapel nave, were manufactured in Lisbon and laid in the mid-17th century.

The ceiling above the high altar bears the insignia of the University of Coimbra, represented by a Christian figure and the emblems of the three major faculties, according to the old division of the university: Theology, Canon Law, Civil Law and Medicine; the ceiling of nave bears the royal coat of arms, surrounded by the three major archangels: St. Michael, St. Raphael, and St. Gabriel.

The baroque Organ, dating back to 1737 and containing more than 2000 tubes, stands out in the decoration of Chapel. The organ is enclosed in a wooden box covered in gilded engravings and decorated with oriental motifs (chinoiserie). Comissioned by King John V, this organ was meant for a much larger church. This explains why it appears to be disproportionate to the space in which it finds itself.It is still used for concerts, masses and other religious ceremonies, and is in perfect working order.

Above the Choir, set aside for the academic music group that plays during Sunday masses, is the royal tribune, the space with a privileged view of the Chapel where the royal family would attend ceremonies.