When Charles abdicated his Spanish crowns in 1556, he retired from Brussels to the remote monastery of Yuste in Spain. There he summoned Don Luis de Quijada to return as majordomo. In the summer of 1558, Quijada brought Magdalena and Jeromín to Yuste, where Charles, on several occasions before his death that September, saw his son, now a youth of eleven. In a codicil to his will, Charles had made provision for Jeromín, and expressed hope that he would enter the clergy and pursue an ecclesiastical career.

Charles' son and heir, Philip II of Spain, returned from Brussels in 1559, aware of his father's will. Settled in Valladolid, he summoned Quijada to bring Jeromín to a hunt. When Philip appeared, Quijada told Jeromín to dismount and make proper obeisance to his king. When Jeromín did so, Philip asked him if he knew the identity of his father. When the boy did not know, Philip embraced him and explained that they had the same father and thus were brothers. Philip, however, was strict regarding protocol. He was not addressed as "highness", a form reserved for royals and sovereign princes. In formal style he was "your excellency", the address used for a Spanish grandee, and known as Don Juan de Austria. Don John did not live in a royal palace, but maintained a separate household with Luis and Magdalena Quijada now heading his service. Philip allowed Don John the incomes allocated to him by Charles so that he might maintain the status proper to the son of an emperor and brother of a king. In public ceremonies, Don John stood, walked or rode behind the royal family, but ahead of the grandees.

Philip's new queen, Elisabeth de Valois, was only a year older than Juan, and his ill fated son by his first marriage, Don Carlos, only two years older. Often in the company of the lively young set was Don John's half - sister Joan, Princess of Portugal, a dozen years his senior. At the baptisms of his nieces, Elisabeth's daughters, Isabella Clara Eugenia and Catherine Michelle, it was Don John who carried the infants to the baptismal font. During and after the battle of Lepanto Don John was addressed in letters and in person as "Highness" and "Prince".

Philip, following the directions of Charles V, sent Don John to the Complutense University in the company of Don Carlos and Alessandro Farnese, Prince of Parma and son of Charles V's other acknowledged illegitimate child, Margaret of Austria, Duchess of Parma (1522 – 86). This was meant to be a preparation for Don John in his ecclesiastical career. At Alcalá in 1562, Carlos suffered a fractured skull that had a deleterious effect on his personality. In 1565, Farnese left to be married in Brussels, where his mother was Regent of the Low Countries. From Farnese, Don John is said to have learned womanizing and, in time, acknowledged two illegitimate daughters, one in Spain, the other in Naples.

The former, Ana de Austria (1568 – 1610), daughter of Ana de Mendoza y Lacerda, 1st Princess of Melito and 1st Duchess of Francavilla, became an abbess; the latter, Juana de Austria (11 September 1573 – 7 February 1630), after years in a convent, married an Italian nobleman, Francesco Branciforte, Prince of Pietraperzia (c. 1575 – 1622) in 1603. They had a daughter Margherita Branciforte, Princess of Butera (d. 24 January 1659, Rome), who married Federico Colonna (1601 – 25 September 1641) and had one son Antonio Colonna, Prince of Pietrapersia (1619 – 1623).

Don John allegedly sired an illegitimate son from a liaison with Zenobia Sarotosia while in Italy. The child is said to have died at childbirth (c. 1574), although it was rumored that Philip had a hand in the unfortunate death of the child. Don John also had a son by his marriage to Hillegond van Veen. The marriage and son, Johannes, were kept secret due to Philip's warning and the politics of the time. The son stayed with his mother after Don John's death and is said to have been brought up in a monastery.

When news reached him at Christmastide of the revolt in Granada of the Moriscos (Moors who had been forced to convert to Christianity), he volunteered to serve in any capacity. The local grandees in charge, the Marquis of Mondéjar in Granada and the Marquis of los Vélez in Murcia, soon fell out over matters of tactics, strategy and the place of clemency. The revolt spread and aid came from Barbary and the Turks. In April 1569 Philip appointed Don Juan commander - in - chief with Quijada as his chief adviser.

In Granada, Don John built his forces with care, learning about logistics and drill. Requeséns and Santa Cruz patrolled the coast with their galleys, limiting aid and reinforcements from Barbary. In December Don John unexpectedly took the field with a large and well supplied army. First clearing rebels from near Granada, he then marched east through Guadix, where veteran troops from Italy joined him, bringing his numbers to 12,000. In late January he assaulted the rebel stronghold of Galera. Fighting was long and hard and casualties heavy. When Galera fell, Don Juan had it leveled and salt ploughed into its soil. The surviving inhabitants were sold into slavery.

As the campaign continued, a musket ball grazed Don John's helmet in a skirmish, while Quijada was fatally wounded at his side. Philip sympathized with Don John's distress at the loss of Quijada, who had been like a father to him, but admonished him that generals should not be in the thick of combat, but take a safe position from which to direct the battle. His troops, however, came to see Don John as more akin to his father Charles V than his famously desk bound brother Philip. Increasingly, they addressed Don Juan as Your Highness. The example of Galera and Don John's determined advance intimidated other Morisco villages, which soon began to surrender to Don John's superior forces. Through 1570 the revolt gradually sputtered out as its leaders quarreled, sought individual advantage, and murdered each other, while the Turks and their Barbary allies turned to the invasion of the Venetian colony of Cyprus. To eliminate the possibility of further revolts in Granada, Philip dispersed its Moorish (Morisco) population in small groups among the Old Christian towns and villages of the Castilian hinterland, reportedly hoping they would assimilate. Eventually, Philip III would order the expulsion of all Moriscos from Spain in 1609.

The War of Cyprus became the focus of Spain’s attention after Pope Pius V sent an envoy to urge Philip to join with him and Venice in a Holy League against the Turks. Philip agreed and negotiations opened in Rome. Among Philip's terms was the appointment of Don John as commander - in - chief of the Holy League armada. While he agreed that Cyprus should be relieved, he was also concerned to recover control of Tunis, where Turks had overthrown the regime of Philip's client Muslim ruler. Tunis posed an immediate threat to Sicily, one of Philip's kingdoms. Philip also had in mind the eventual conquest of Algiers, whose corsairs posed a constant nuisance to Spain. Charles V had tried, and failed, to take it in 1541.

While Don John finished the pacification of Granada, negotiations dragged on in Rome. In the summer of 1570, with an allied fleet of Venetian galleys, Philip sailed for Cyprus, under the pope's admiral Marcantonio Colonna. In charge of Philip's contingent was the Genoese Gian Andrea Doria, a great - nephew of the renowned Andrea Doria. On reaching the Turkish coast in September, Colonna and the Venetians wished to press on to Cyprus while Doria argued that the season had grown too late. Then news arrived that Nicosia, the capital of Cyprus, had fallen, and only the port of Famagusta held out. Sickness hit the Venetian fleet and a consensus grew that it was best to return to port. The weather turned ugly and while Doria reached port in good order, the Venetians were storm - battered. Among the Christian allies, animosities became open while the Turks tightened their siege of Famagusta.

The Venetians repaired their galley fleet and readied six heavily armed galleasses. The Pope hired twelve galleys from the Grand Duke of Tuscany. The dukes of Savoy and Parma also provided galleys, and Alexander Farnese sailed in one. When the League was formally signed in May, Don John was designated commander - in - chief and given his many instructions by Philip. With the instructions came a warning not to involve himself with women, which, among other instructions, were ignored by Don John. It was late July before he sailed with the Spanish squadron from Barcelona, and mid - September before the entire Holy League armada got underway from Messina. Don John was determined to fight, rallying allies, quelling their mutual suspicions and inspiring enthusiasm for what he referred to as "a holy cause".

Don John found the Turkish fleet at Lepanto in the Gulf of Corinth. After some debate, the Turks chose to fight, even though they had been at sea all summer and disbanded some of their people. They had the larger fleet, nearly 300 to Don John's 207 galleys and six galleasses. On 7 October 1571, the Turkish fleet emerged into the Gulf of Patras and took battle formation. Bringing his fleet through islets known as the Curzolaris (now mostly lost to the silting of the shoreline), Don John deployed his armada into a left wing under Venetian command, a right wing under Doria, a powerful center or main battle under himself, and a strong rear guard under the Marquis of Santa Cruz. In all four formations were galleys from each of the participating states. Two galleasses each were assigned to the wings and center. Around noon the battle commenced. The cannonade of the galleasses disrupted the Turkish formations as they pressed to the attack, and the bigger and more numerous guns of the Christian allies did devastating damage as the Turkish right and center closed to board. In the seesaw fighting on decks, the allies prevailed. Among their wounded was Miguel de Cervantes, who would later in Don Quixote describe combat aboard galleys and call Lepanto the greatest occasion known to the centuries, past, present and future.

The Turkish remaining under Uluj Ali, the governor general of Algiers and their best admiral, tried to out - maneuver Doria's wing, drawing it away from the League center. When a gap appeared between Doria and the center, Uluj Ali made a quick turn about and aimed at the gap, smashing three galleys of the Knights of Malta on Don John's right flank. Don John came around smartly while the Marquis of Santa Cruz hit Uluj Ali hard with his rear guard. Uluj Ali himself and maybe half his wing escaped. The victory was near total, with the Turkish fleet destroyed and thousands of veterans lost. The League's losses were hardly negligible, with over 7000 dead. In the evening a storm broke and the victors had to head for port, while sporadic Greek uprisings were ruthlessly suppressed by the Turks. During and after the battle of Lepanto, Don John was addressed in letters and in person with "Highness" and "Prince". This was in contradiction to the initial protocol and address by Philip. There are no records to indicate if Philip gave Don John these honors.

All looked forward to the campaign of 1572, but events in France, with the growth of Protestant Huguenot power, seemed to threaten Philip's Low Countries, where the Duke of Alba had restored an uneasy order. Philip ordered Don Juan to hold his part of the Holy League armada at Palermo, prepared to respond to events in France. Colonna took the rest into Greek waters, but achieved nothing. By the time Don Juan joined his allies in late summer, and attempted to take the Turkish citadel of Modon on the Peloponnesus (then known as the Morea), the Turks had too many reinforcements in place.

Don John wintered in Naples, from which he made his first visit to his half - sister Margaret, Duchess of Parma, in l'Aquila. They had corresponded for some time and would continue to do so. He confided in her about his love affairs, and after the birth of an illegitimate daughter had her delivered to Margaret's care. His relations with the new Viceroy of Naples, Cardinal Granvelle, an old and experienced diplomat, were not easy, but he did learn more of statecraft and the problems of northern Europe. At some point he began to entertain fantasies of liberating the Catholic Mary, Queen of Scots, held in prison in England for treason, and perhaps marrying her and taking England's throne. Such an idea received encouragement in Rome. In May 1572 Pope Pius V died; by early 1573, the Venetians, distrusting Philip II, made a separate peace with the Turks. Don John put his energy into the recovery of Tunis, which he achieved that fall, restoring a client Muslim ruler. Against advice from Madrid to raze Tunis and destroy its harbor and the great fortress of La Goletta, erected by Charles V after his conquest of Tunis in 1535, Don John chose to keep La Goletta, which had held out in 1570, and build a new fortress inside Tunis to dominate the city. He and the Marquis of Santa Cruz planned next to take Algiers, while critics, including Granvelle, hinted that Don John dreamed of becoming King of Tunis.

By 1573, the revolt of the Low Countries had revived and Don John found himself increasingly short on funds. While his name had been bruited for the post of Governor General to succeed the Duke of Alba, it was the older Requeséns who received it. In 1574, unrest spread in Genoa against Doria and his dominant party. Genoa was Spain's chief banker, and Don John found himself preoccupied by Genoese politics. That summer a huge Turkish armada under Uluj Ali struck Tunis and within weeks, both La Goletta and the new city citadel were lost. Don John had hurried to Palermo and assembled all available forces, but it was too little and too late.

He came to feel abandoned and though Philip had enhanced his authority over the viceroys of Naples and Sicily, who had not always proved cooperative, he returned to Madrid at the beginning of 1575 to confer in person with Philip and the Council of War. He claimed to be unaware that orders had been sent that he remain in Italy. On his return there, he once again became entangled in Genoese politics, which had become more turbulent after Philip declared bankruptcy. Wars on two fronts, the Low Countries and the Mediterranean, had overtaxed his finances, and he suspended payments on debts prior to their renegotiation. With Santa Cruz in Naples, Don John could undertake little but occasional punitive strikes against Tunisian corsair lairs with his reduced fleet.

Don John and Santa Cruz had planned a larger campaign for 1576, when in May he received the long dreaded orders to proceed directly to the Low Countries as Governor General, following the death of Requeséns. In Rome he once more received encouragement in his schemes to liberate the Queen of Scots, making the governor generalship more attractive. In northern Italy he halted, and sent his secretary Juan de Escobedo to Spain, to secure more money and win Philip's consent for his plans for the Queen of Scots. When by late summer Escobedo had not returned, Don John sailed for Spain. His shocked brother met with him privately at the Escorial. Philip seems to have accepted Don Juan’s plans for the Queen of Scots, but only after he had secured peace in the Low Countries. Because he was short of money, Philip expected Don John to achieve peace through diplomacy and negotiation. Having received his instructions, Don Juan and a few companions made a dash for the Low Countries across France, rent by religious civil war. Fearing Protestant assassins, Don John reportedly wore the disguise of a Moorish slave.

While grievances in the Low Countries were many, at the heart of the revolt was religion, Calvinism on the rebel side, Roman Catholicism on Philip's. Don John was a convinced Catholic, had crusaded for the Cross against the Muslim Turks and regarded Protestants simply as heretics. But some, particularly in the Low Countries, argued that limited toleration might be the only feasible solution for the revolt. Of the historic seventeen provinces, Holland and Zeeland were largely in rebel control. The rebels made William, Prince of Orange their leader. After Requeséns's death, Philip's army of Flanders, its pay in arrears, mutinied and began to maraud for loot and stores in the provinces not under rebel control. The States General of the Low Countries assembled at Ghent while local authorities raised troops for self - defense. Delegates from the rebel provinces met with their fellows to find grounds for a common cause. In early November, mutineers sacked the city of Antwerp in what came to be called "the Spanish Fury". At Ghent the delegates signed a Pacification which granted limited tolerance and authorized the raising of an army to deal with Philip's mutinous troops, whom they demanded be removed.

Don John got the news of the sack in Luxembourg soon after his arrival, and learned that his acceptance as Governor General depended upon his acceding to the Pacification of Ghent. Don Juan negotiated from Luxembourg, separate and loyal. He knew that removing the army would deprive him of the means to invade England, so he suggested that if the troops must go, it would be best to send them by sea and asked the States General to provide shipping.

The States General demurred and insisted they depart overland. They eventually did, marching south loaded with their plunder. With the army departing, the matter of toleration became the chief sticking point, with rebel demands that the Calvinist faith be practiced openly in the rebel provinces and be tolerated in the others, according to local initiative. These were terms neither Philip nor he would accept, but as Don Juan had no means of using force, he could only temporize. He issued a Perpetual Edict accepting the Pacification, but, confident that Catholics still remained the majority in the Low Countries, stipulated that panels of theologians hammer out the matter of toleration, with all to abide by their decisions.

As most were tired of wrangling and bloodshed, the States General accepted Don John as Governor General. In May 1577, he made his Joyous Entry into Brussels, promising to respect its historic privileges, which by extension had become the privileges of the seventeen provinces. As he assumed his office, he had to deal with the problem of his widowed mother in Ghent who scandalized her neighbors by her conduct. She had had two sons by Kegel, of whom one drowned and the other served in the royal army. At times she disowned Don John, despite receiving a government pension on his behalf. He eventually persuaded her to journey to Italy and meet Margaret of Parma. Her ship took her instead to Spain, where she was eventually settled on Escobedo's property near Santander and lived till 1598.

Don John agreed to meet with the rebel leader, the Prince of Orange, but the meeting never took place. Reports came from reliable sources that militant Protestants aimed to assassinate him. He took them seriously and in July used the visit of Marguerite de Valois, Queen of Navarre, to Spa as an excuse to meet her near Namur. There were stories that on his dash through France they had a secret tryst in Paris. After she resumed her journey, Don John and his selected companions seized the citadel of Namur in violation of the Perpetual Edict. He sent Escobedo to Spain to explain to Philip the impossibility of gaining an acceptable peace and calling for the return of the army. The States General declared war on Don John. Don John, Farnese and the army had routed the States General's army at Gembloux that January. On the news of Escobedo's murder Don Juan was perplexed, and knew not whom to believe. With the murder Don John did not see any future in his wishes to become a monarch in his own right. He is said to have lost motivation and trust in Philip and his intentions. During his stay in present day Belgium he met Hillegond van Veen, daughter of Cornelis Jansz van Veen, Chief magistrate of Leyden and descendant of the Duke of Brabant.

Don John fathered a son, Johannes, with Hillegond van Veen. Tired and increasingly ill, he campaigned through the summer with mixed success, but failed in his attempt to take Brussels, after receiving a setback in the Battle of Rijmenam on 2 August 1578. He did win more and more of the Catholic nobles and towns to the royal cause. As ever money was a problem, and he felt his life was being doled out in bits and pieces, and complained to friends of the endless rainy weather. He married Hillegond quietly without obtaining approval from Philip. In September he pulled the army into camp near Namur to regroup.

On 1 October 1578, he reportedly died of what contemporaries called camp fever (typhus). His army gave him a funeral due a hero. He had appointed Farnese his successor as Governor General, which Philip confirmed.

His body was dissected, returned to Spain, reassembled and placed by Philip to rest in the unfinished crypt of the Escorial, not far from their father. In time the body had its own niche and a 19th century marble effigy. Philip, reviewing Don John's papers, found no evidence of disloyalty and put Pérez under arrest.

Don John of Austria's life inspired the 1835 play Don Juan d'Autriche by Casimir Delavigne, which served in turn as a source for two operas, Don John of Austria by Isaac Nathan in 1847 and Don Giovanni d'Austria by Filippo Marchetti in 1879. Lepanto remains his great triumph. G.K. Chesterton in 1911 published a poem, Lepanto, in which he dubbed Don Juan "the last knight of Europe".

In 1956, Louis de Wohl published The Last Crusader: A Novel about Don Juan of Austria, whose ambitions, above all for the Queen of Scots, tend to obscure his talent for statecraft and ability to lead. Frustrated by the religious factiousness in the Low Countries, he began the policies that Farnese would follow in keeping the ten southern provinces, comprising present day Belgium, Luxembourg and much of the French Netherlands, Roman Catholic and loyal to Philip, and limiting the revolt to the northern seven heavily Protestant areas which eventually became the Dutch Republic.