The building that exists today was the result of works directed by Marcos Pires and completed by Diogo de Castilho. It underwent minor remodeling in the 17th and 18th centuries. The Royal chapel dedicated to S. Miguel was also the headquarters of the Confraria of lenses and students under the invocation of Nossa Senhora da Luz. Its architectural structure is Manueline, a decorative style visible mainly in the windows of the central nave and in the cruise arch.

When the University acquired the Palace, it also acquired the Chapel, keeping it a royal privilege. The tiled covering of the chancel dates from 1613, and the nave was covered with “carpet” tiles that were manufactured in Lisbon. The ceiling painting is due to Lisbon's Francisco F. de Araújo, who executed it at the end of the century. XVII. Later it was renewed and the royal shield modernized.