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

This chapel formed part of the parish of St. Catherine of Żejtun, and it stood on land which belonged to Salvu Burlò.

[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.