Having conquered nearly the entire island, the Ottomans, under the command of Gazi Hüseyin Pasha, appeared before the walls of Candia in the summer of 1647. They encamped to the west of the fortress, near the river Giophyros, and began preparations for the siege.

The Venetian forces were commanded by General Francesco Morosini, the last defender of the city. The Cretan citizens stood with heroism and self-sacrifice alongside the Venetians, defending their freedom. One of the first actions of the besiegers was to cut off the city’s water supply via the Morosini aqueduct, which brought water from Archanes. The Ottomans also attempted to approach the fortress through tunnels (mines) and successive trenches parallel to the sections of the fortifications they sought to assault. These works were executed by skilled sappers, mostly Armenian miners. The technique initially yielded no decisive results, as the method was still underdeveloped. The use of mines by the attackers and countermines by the defenders, combined with relentless bombardment, would define the prolonged siege. Heavy artillery arrived in March 1648 and was emplaced on the heights surrounding the city. For the following twenty-one years, the sea would remain the inhabitants’ only means of escape.

The Ottomans initially chose to attack from the south and southeast, targeting the stronger bastions (Vitturi, Jesus, Martinengo), mistakenly believing that the high ground beyond the ditch would confer an advantage. The first fierce assault, in June 1648 against the bastion of Vitturi, was successfully repelled by the defenders of the external fort of Saint Demetrius. After repeated failures, Hüseyin withdrew to the heights of Marathitis, where he established a permanent camp.

Attacks resumed the following year (1649), from August to early October, along the same sector on the southwestern side of the fortress, from the Martinengo bastion to the Pantokrator bastion, and against the corresponding external fortifications, notably the opera Moceniga, without success.

As the siege was clearly destined to be prolonged, the Ottomans sought to establish organised strongholds and shelters. By Sultan’s decree, on 28 February 1649, orders were issued to construct three small forts around Candia’s walls: one to the east, near the lazaretto; one to the south; and one to the west of the Giophyros river. At the same time, a fourth, larger fort was built on the heights of Broussa, at the site of the present settlement of Fortezza, which became the Ottoman headquarters. This fortress was named Enantia, or New Candia, also known as Inadiye or Kale-i-Cedit (New Fortress).

From 1649 to 1666 the war reached a stalemate. The city remained blockaded, and maritime access became increasingly difficult. In 1666 the situation changed dramatically. The Sultan had already recalled and executed Hüseyin, blaming him for the failure of the siege, and appointed as commander the capable, ambitious, and ruthless Ahmed Pasha Köprülü, who would prove decisive for the city’s fate. Köprülü fortified the artillery positions, moved his headquarters to the Giophyros fort, protected it with a ditch to the east, established a cannon foundry near Knossos, and a powder magazine near Fortezza, while ensuring the army’s supply through the ports of Tsoutsouros, Matala, and Ierapetra.

On 28 May 1667, a new assault began with three hundred guns on the southwestern section of the fortress, from the Martinengo bastion to the Saint Andrew bastion. The Ottomans destroyed the Pantokrator outwork, captured the external fort, and entered the ditch, applying immense pressure on the defenders. Attacks continued until November.

On 15 November 1667, the Venetian-Cretan engineer Andrea Barozzi defected to the Ottoman camp, providing Köprülü with detailed information on the construction and condition of the fortress, revealing the vulnerability of the two seaward bastions, Sabbionara and Saint Andrew. Due to their position, these bastions were incomplete, possessing only a single orecchione and a low gun platform, and were lower than the other bastions. Crucially, the Venetians could not repel undermining attacks with countermines, as the Saint Andrew bastion was built on rocky ground, and the Sabbionara bastion on sand. Barozzi also suggested improvements to the parallel trench system. Under his guidance, the Ottomans revised their tactics, directing their artillery fire toward the two northern ends of the landward fortifications.

In November 1667, the bombardment of the Saint Andrew bastion commenced, while from 10 December external forts were constructed opposite the two seaward bastions. The defenders recognised the tactical shift but could not counter it.

On 11 June 1668, a new assault was launched against the Sabbionara and Saint Andrew bastions, causing serious breaches. By January 1669 the situation had become desperate. The Saint Andrew bastion and the first line of defence had been captured, and the besieged had withdrawn to the second line. On the Sabbionara bastion, insignia of the Janissary corps flew in place of the flag of Saint Mark. The seven Janissary regiments prepared to raise their flags, the famous Seven Axes, atop and to the west of the bastion.

The city’s fate was now sealed. The heroic sortie of the French allies, under Admiral Duke de Beaufort and the Duke de Navailles, failed, as did the bombardment of Ottoman positions by the Christian fleet. The explosion that sank the French vice-flagship La Thérèse marked the end of the attempt.

Faced with the threat of pillage and massacre, the last heroic defender of Candia Francesco Morosini, opted for surrender. According to the treaty signed after protracted negotiations on 16 September 1669, the Venetians ceded Crete to the Ottomans, retaining only the fortresses of Gramvousa, Souda, and Spinalonga. The city’s inhabitants were allowed to leave, taking their arms, heirlooms, and archives.

Thanks to this clause, the state archives of Candia were preserved and transferred to Venice. Morosini was later accused of mishandling the surrender, but ultimately acquitted. Enduring testimony to his devotion may be found in the subjects adorning his banner—painted by the renowned Cretan artist Victor, now in the Museo Correr, Venice—and in the dedication of his coat of arms and coronet to the Virgin Mesopanditissa, the miraculous icon of Candia, preserved in Santa Maria della Salute.

When Ottoman troops entered Candia on 4 October 1669, they found a deserted city.