Though it was hoped that he would enter the church, the handsome and spirited Don Juan expressed a desire to embark on a military career, and Felipe acceded to his wishes. In the summer of 1568 Don Juan had his first brief experience in warfare, fighting Moorish pirates in the Mediterranean, and he was then appointed in March 1569 commander in chief of Spanish forces attempting to subdue the rebellious Moriscos, or Christians of Moorish ancestry, in Granada. Felipe then appointed him in 1571 to head the naval forces of the Holy League of Spain, Venice, and the pope against the Ottoman Turks in the eastern Mediterranean.

By the prestige of his royal name, and by his enthusiasm, Don Juan was able to impose a temporary unity of purpose on the quarreling admirals of the league and to form the several fleets into an effective fighting unit. In the Battle of Lepanto (Oct. 7, 1571) the allies virtually annihilated the Turkish forces, thereby destroying the myth of Turkish invincibility. The victory of Lepanto also fired Don Juan's personal ambitions for further campaigns against the Turks, but Felipe would only allow him to conquer Tunis (1573). The city was, however, reconquered again by the Turks the following year.

For several years Don Juan continued to chafe under the restraints his prudent brother imposed upon him, but in 1576 he was appointed governor-general of the Netherlands, then in open revolt against Spanish authority. Don Juan was at first reluctant to accept this difficult post and took it only on condition that he would be allowed to invade England and wed Mary Stuart, the Scottish queen then in captivity in England. In the Netherlands he signed the Perpetual Edict with the rebels (February 1577), by which, in exchange for rebel recognition of Don Juan as governor and restoration of the Roman Catholic religion, Spanish troops were to be removed. The provinces of Holland and Zeeland did not accept the return to Catholicism and refused to recognize Don Juan's authority. Don Juan then assumed the more congenial role of soldier and resumed the war by capturing Namur.

Don Juan's last months were marred by the murder of his secretary, Juan de Escobedo, who had aroused Felipe's enmity. The monarch's complicity in the crime was strongly suspected. Don Juan felt that he had lost his brother's confidence and was also hampered in his war in the Netherlands by lack of adequate financial and military backing. His death in 1578 released him from an increasingly intolerable position.