The exact date when Saint Margerita Chapel was built is unknown but it was around the event of the Great Siege of Malta.

It was mentioned for the first time in an inscription of Monsignor Pietro Dusina in 1575, when he was sent by the papacy to inspect the sparse chapels on the Maltese islands.

Visitavit etiam alliam Ecclesiam ruralem sub vocabulo Sanctae Margaritae in pertinentia Bircalcariae, constructam in contrata Arar, quae habet altare, caret portis ligneis, rectore, introitibus, et omnibus alija necessarijs, sed Salvus Calleja ex devotione sua in die festivitatis in eadem celebrari facit missam rantum.

[1] Bishop Michele Girolamo Molina in 1658 observed that it suffered serious neglect while abandoned, and Father Giacomo Pullucino took the initiative to restore the chapel,[2] finishing in 1666.

[3] Pullicino died in 1680 and was allowed to be buried inside the chapel, as documented by Bishop Miguel Juan Balaguer Camarasa, the parish priest of Birkirkara.

[1] During World War II several families relocated to San Gwann from the Valletta and the surrounding cities and suburbs, for safety's sake.

[7][8] Santa Margerita Chapel is scheduled as a grade 1 national monument since 1994 by the Malta Environment and Planning Authority (MEPA).