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Governor of the Netherlands (1567–73)

On December 26, 1566, Alba received the Golden Rose, the blessed sword and hat granted by Pope Pius V, through the papal brief Solent Romani Pontifices, in recognition of his singular efforts in favor of Catholicism and for being considered one of his champions.

From August to October 1566, the " Iconoclasm " (Dutch: Beeldenstorm) took place in the Netherlands, during which Calvinist mobs attacked and destroyed numerous Catholic monasteries and churches, ransacking tombs and destroying statues. To tackle the civil and religious rebels, King Philip II sent Alba to Brussels on 22 August 1567, at the head of a powerful army. Upon arrival, he replaced Margaret of Parma, the sister of the Spanish king, as head of the civil jurisdiction. He decided that the local nobility was in open rebellion against the king and supported the new Protestant teachings, heresy in the Catholic view.

A few days later, on 5 September 1567, Alba established the " Council of Troubles ", popularly known in the Netherlands as the "Court of Blood," to prosecute those responsible for the riots of 1566, especially those deemed heretics. Alba also targeted the local Catholic nobles who favoured dialogue and who opposed outside intervention. Two of the three heads of Flemish nobility, the Count of Egmont, a Catholic General for Philip II, who had led the cavalry that defeated the French at the Battle of San Quentin, and Philip de Montmorency, Count of Horn, were arrested and the court sentenced both counts to death. The Mayor of Antwerp, Anthony van Stralen, Lord of Merksem and Jan van Casembroot were other famous victims of the bloody repression, along with a large group of other apostates. Those condemned were executed on 5 June 1568 in the Town Hall Square in Brussels. Alba had little confidence in conventional Flemish justice, which he perceived as sympathetic to the defendants, and witnessed the executions in person. He would later become equally mistrustful of the local helpers of the Council of Troubles as possibly having their own agendas.

The maintenance of the troops in Flanders entailed substantial economic costs. The Duke imposed new taxes on the population and reformed its laws. Some cities, including Utrecht, refused to pay and declared a rebellion, which quickly spread throughout the Netherlands. William the Silent, the prince of Orange, enlisted the help of the French Huguenots and started to actively support the rebellion. William and the Huguenots took many Dutch cities. The Spanish troops advanced under banners with the Latin legend Pro lege, rege, et grege, which in English means For the law, the king, and the people.In 1572 the Spanish army carried out the Spanish Fury at Mechelen, retaking and sacking the city after the rebel garrison had left. From there, they retook Zutphen and Naarden. The Spanish Siege of Haarlem, characterized by brutality and savagery on both sides, culminated in the surrender of the city and the execution of all the garrison, estimated at 2,000 men. The subsequent Siege of Alkmaar was unsuccessful however: it was the first defeat in a full scale engagement for the Spanish troops during the Dutch revolt. The prolonged military campaigns and the harsh repression of the rebel citizenry earned the 3rd Duke of Alba the nickname "The Iron Duke" in the Netherlands, and he became an important element of the anti-Spanish Black Legend. His reputation was used for propaganda purposes by rebel statesman Philips of Marnix, Lord of Saint-Aldegonde to further strengthen anti-Spanish sentiments in the Netherlands.

In spite of continuous military action, the political situation in the Netherlands had not turned in favour of the Spanish crown. After five years of repression, more than 5,000 executions and numerous complaints to the Spanish court, Philip II decided to change policy and relieve the Duke. The monarch sent Luis de Requesens to replace him. De Requesens tried to appease the situation by giving concessions to the rebels. Alba returned to Spain in 1573.

Nevertheless, the Duke still had influence in the Royal Council. Alba belonged to the conservative Spanish faction called Albistas or imperialists. This faction included the Inquisitor General Fernando de Valdés y Salas, the House of Pimentel, the Duke de Alburquerque and other members of the House of Álvarez de Toledo. The Albistas advised the king to take a firm stand in the Netherlands. The Albistas' hardline position was hotly contested by the liberal Ebolistas or humanists, led by Ruy Gómez de Silva, prince of Éboli and his secretary Francisco de Eraso. After the death of the prince of Éboli in 1573, the royal secretary Antonio Pérez went on to lead the liberal faction and began his association with Ana de Mendoza de la Cerda, Princess of Éboli. Against the Albistas' urging, King Philip II himself publicly acknowledged that "it is not possible to carry Flanders forward by way of war." Political concessions by Luis de Requesens failed to end the rebellion in the Netherlands and hostilities soon resumed. These failures of the Ebolistas to end the Dutch revolt raised the distrust of the king, and Philip II again granted the Duke of Alba an important position in court.