Since 1373 there was a chapel dedicated to St John the Almsgiver situated on the site known as ta’ Għuxa between St Helen’s Gate and Għajn Dwieli. The name ta’ Għuxa (to live) possibly referred to a site where a hermit once lived on alms, and which later developed into a garden. Historians Giovanni Francesco Abela and Gian Pietro Agius De Soldanis refer to a wooden statue of St John the Baptist that was found in this chapel and believed to have been brought from Rhodes by the Order when they came to Malta in 1530.

The original chapel was demolished in 1678 to make way for the Cottonera Lines and a new chapel funded by prior Fra Pierre Viany was erected on higher ground in 1680. The Italian Baroque painter Mattia Preti left two of his masterpieces in this chapel and these can now be found at the National Museum of Fine Arts.

The Chapel of St John the Almsgiver was extensively damaged during the Second World War and although it has since been restored, it has never again been used for religious services.