The octagonal chapel is a miniature museum in itself. It can be found on the first floor of the museum. One of the most curious features of this chapel is its fake dome, composed of eight arched stretchers covered with canvas onto which painted architectural features and decorative motifs form a trompe l’oeil effect of an illusion of a Baroque dome. The five main paintings within the chapel were commissioned by Bishop Paul Alpheran de Bussan to the court painter Antoine Favray.
In the late 1740s Favray worked on a set of five paintings for the chapel of the Seminary in Mdina commissioned by Bishop Paul Alpheran de Bussan. The main altarpiece here shows The Annunciation, with its lyricism and chromatic qualities, one of the most precious relics. This painting is flanked by St. Peter and St. Paul. Paintings of St. Francis De Salle, and St. Carlo Borromeo may also be appreciated by a visitor of the chapel.