This chapel is located in the noble residential floor, which is on the south side of the Seminary. It has a stunning gilt carved retable of Rococo style.

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The São Miguel Chapel is a reliquary chapel. There are twelve reliquaries distributed in the columns, each of them containing the relics of twelve apostles. Some of these reliquaries were either stolen or damaged during the French invasions.

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The story tells that it was built shortly before 1765, which is the year that the construction was finalized. The construction project is attributed to Giacomo Azzolini, a Bolognese artist in charge of the construction.