After the Great Siege, Laparelli rebuilt the fort of St. Elmo on the original plan and footprint. The fort was enlarged and fitted with barracks. The demolished ravelin was replaced by a deep ditch, which was enclosed within two walls in the second half of the sixteenth century.

Fort St Elmo was not included in the line of fortifications protecting Valletta and this led to the construction of the Vendôme Bastion. In 1687 the Flemish military engineer Carl Grunenberg submitted a report and a masonry model in which it was suggested to construct at least three bastions on the ledge of the cliff facing the fort. Eventually the Carafa bastions created a new enceinte around St Elmo.

In the first half of the eighteenth century the northern ramparts were replaced with two strong walls which joined completely the cavalier to the body of the fort. The ditch was filled in and thus enabled grounds on which to build a large barrack block designed by Mondion. The guns of St Elmo would remain silent when the French army arrived in the harbour in 1798.