The building that exists today is the result of works directed by Marcos Pires and finished by Diogo de Castilho. The Chapel underwent small renovations in the 17th and 18th centuries.
The royal chapel dedicated to St. Michael was also the headquarters of the Brotherhood of Professors and Students under the invocation of Our Lady of Light Its architectural structure is Manueline, a decorative style mainly visible in the huge windows of the aisle and transept.
When the University acquired the Palace it also acquired the Chapel, maintaining its royal privilege.
The tile flooring of the main chapel dates from 1613, and the aisle is covered with "carpet" like tiles that were manufactured in Lisbon. The painting of the ceiling was made by Francisco F. de Araújo by the end of the 17th century.
Later it was renovated and the coat of arms was modernized.