With the establishment of the Order of St. John in Malta in 1530, security against pirate attacks somewhat improved. The Order engaged in the practice of 'corso,' employing its renowned and glorious galley fleet, justifying it as an extension of its struggle against the Infidel. The Order fortified the main harbour region of the island with costly fortification schemes, making assaults against them nearly impossible. However, until the early 1600s, most of the southeast coast and the island's extremities, along with the smaller islands, remained unprotected. During this period, scattered coastal watch posts were maintained mainly by the militia to detect any impending attacks. Theoretically, these posts were meant to raise the alarm in time for the rural population to seek refuge in the walled towns, but this plan did not always succeed.

​

A significant incident illustrating the vulnerability of the island's defenses occurred in 1614 when a large Turkish force led by Khalil Pasha, comprising around sixty vessels, landed 5,000 men in the then-unguarded St. Thomas Bay. This landing took place after the Turks were repelled in Marsaxlokk due to fierce resistance from the newly constructed Fort St. Lucian (1610). During this attack, the Turks pillaged various villages and penetrated deep into the island's hinterland until they were compelled to withdraw by a robust militia force led by members of the Order.

​

Recognising the vulnerability of its southern harbours to pirate attacks, the Order took measures to address this issue. In 1610, they built a massive stone fort roughly in the middle of Marsaxlokk Bay, named after St. Lucian, a Christian martyr. In 1614, Grand Master Alof de Wignacourt aimed to eliminate the inherent dangers of unopposed landings at both M’Scala and St. Thomas Bay by constructing another powerful fort on a spur of land between the two bays. This new fort was named after St. Thomas and followed the design of the forts built to protect St. Paul’s Bay and Marsaxlokk.

FORT OR TOWER? 

Despite being commonly known as a tower, St. Thomas was designed to function as a garrison fort capable of withstanding a siege of 40 days if well provisioned with food and ammunition. In official reports from the time, the structure is more commonly referred to as ‘forte’ or ‘fortino,’ meaning a small fort (although St Thomas Tower is the Largest Tower in Malta).

​

It was previously believed that the tower was designed by Vittorio Cassar, the Order’s resident military engineer and son of the renowned Maltese engineer Girolamo Cassar. However, this is now uncertain, as Cassar passed away in 1609, and St. Thomas Tower was constructed five years later. It's plausible that, in building a series of large coastal forts in Malta, the Order looked at prevalent fortress designs of the time and adopted a configuration similar to those being constructed along the Mediterranean littoral for the same purpose. Thus, the design of these forts can be attributed to a movement where different military engineers contributed to evolving a strong, large, defensible artillery structure.

The construction of the new fort, St. Thomas Tower, cost 13,450 scudi. It followed a square plan with projecting square corner towers, classifying it as a star-shaped fort. Built entirely from stone quarried on site, the fort features thick walls measuring around five meters, consisting of two thick skins of ashlar with packed stone rubble in between.

​

The interior comprises two cavernous barrel-vaulted chambers serving as living quarters for the garrison and storage for weapons and ammunition. It includes a water well accessed from inside, a hearth for cooking, and a small underground chamber that may have served as a gunpowder store. One chamber has a small room supported by an arch, potentially serving as a chapel. The interior is illuminated by large vertical windows set into the side walls, with no windows on the front and back.