After Castile captured Gibraltar from the Moors in 1462, friars from the Franciscan order established a presence in the city and constructed a friary and church there.

[dubious – discuss] Francis Carter wrote in 1771: "The Church of the Convent is kept open for Divine Service, and the only one in the town, all other chapels and places of worship having been turned into storehouses to the great scandal of the Spanish and inconvenience of the Protestants.

The Spanish bombardment of Gibraltar caused widespread destruction, and the chapel was not spared; its western end and south transept were destroyed by enemy fire.

[7] The event was recorded in one resident's diary for 19 September 1779: "The cupola of the White Convent was taken down, also the arch and upper part of the Governor's Church.

The chapel was too small to accommodate the rest of the garrison, who held a Church Parade Service in the open air in what is now John Mackintosh Square.

[10] He described the building as "quite an ordinary accommodation" and commented: The plainness of its walls and accompaniments, with the paucity of worshippers who usually convene there, occasions severe strictures on the genius of Protestantism by the superstitious Catholics.

There is no bell to the chapel; and for want of such a summons, a flourish of drums and fifes from a band stationed in Commercial Square announces when the hour of service arrives.

[12] The chapel gained a fresh lease of life in 1844 when it was restored by the Royal Engineers at a cost of £340 3s 3¾d to serve as an auxiliary place of worship for Gibraltar's civilian population.

[13] The Assistant Military Secretary at the time summarised the situation in a letter of 8 March 1844: When the Governor assumed the government, he found the Convent Chapel in a neglected, dark, unwholesome state and a sephulchral nuisance to the residence ...[T]he Bishop and Archdeacon stated to the Governor that the Protestant community at large experienced great inconvenience from the Cathedral being so filled by the military that insufficient space was left for the civilian congregation.

The ammunition ship was destroyed after it exploded at Gun Wharf (now Queensway Quay Marina) while being unloaded, killing 13 people and causing massive damage across the city.

The window in the north transept depicts King George VI, while that in the east wall shows Christ in glory surrounded by the Archangels Raphael, Gabriel, Uriel and Michael.

This arrangement was ended in 1990 when a resident Royal Navy chaplain was stationed at King's Chapel to provide chaplaincy to all three services, supported by civilian clergy.