Notarial documents of the early 16th century suggest that a chapel dedicated to Saint Nicholas existed in the Żonqor area.

[1] This chapel was not well-maintained, and it was not used regularly, which resulted in it being profaned by Bishop Miguel Juan Balaguer Camarasa on 25 March 1659, and again by Lorenzo D'Astiria in 1666.

[1] The present building was built by the lawyer Giovanni Battista Azzopardi Barbara, in order to fulfill the wish of his father, Gian Francesco.

[1][3][4] At some point, a plaque stating non gode l'immunita ecclesias was installed near the doorway to indicate that the chapel did not enjoy ecclesiastical immunity.

[1] The chapel's altarpiece depicts Saint Nicholas wearing a bishop's clothing, and it is attributed to Mattia Preti's bottega.

The original painting is now in the Żabbar Sanctuary Museum, and a copy by Michael Mifsud is located inside the chapel.