The Annunciation Chapel within the museum is a sacred space that originally served the building when it functioned as a seminary. This octagonal chapel is a miniature museum in itself, reflecting the refined taste and vision of Bishop Fra Paul Alpheran de Bussan, whose ambitious project began in 1733.

The bishop commissioned the court painter Antoine Favray to create five exquisite canvases for the main altar, depicting the Annunciation of the Blessed Virgin. Flanking the altar are oval paintings of St. Peter and St. Paul, accompanied by depictions of St. Francis de Sales and St. Charles Borromeo. These works were completed and paid for in 1749. Additionally, a small elliptical sottoquadro portrays St. Francis of Paola, painted by Francesco Zahra (1710–1773).

The smallest altar bears the name of Paulus Alpheran de Bussan, as do the brass candlesticks, while even the door knockers carry his coat of arms—testifying to the personal devotion and care he invested in the chapel. The seminary was so dear to his heart that he ordered his heart to be interred within these walls, commemorated by a marble cartouche bearing an inscription in his honor.

This intimate chapel allows visitors to step into the spiritual and artistic world of 18th-century Malta, where devotion, art, and personal legacy intertwine.