[2] He held important positions in the navy and carried out several military operations in which he had to fight against English, Dutch, French and Barbary forces in the Atlantic, the Caribbean and the Mediterranean.

[2] Later he managed to ascend socially, due to the military prestige he obtained during his naval career and the support of his influential paternal family, the House of Los Vélez.

[6] The marriage ties of his descendants, which he helped manage, also reinforced his social position, as well as that of his children, gaining large possessions for his family in Murcia.

[9] He also had a daughter named Mencía Fajardo de Tenza, who in 1609 married Juan Antonio Usodemar Narváez, lord of the village of Alcantarilla, a fact that initially did not please her father.

[3] In November 1604, he was appointed captain general of the Armada del Mar Océano, replacing the late Admiral Alonso de Bazán.

[15] With this naval force he had the mission of protecting the Iberian coast of the Atlantic and the Strait of Gibraltar, also taking into account that it was the route of arrival of the Spanish treasure fleet.

[20] In May 1609 he delivered a report to the king about the problems in the maintenance of the Spanish ships due to rot caused by inadequately curing the vessels.

With the Pax Hispanica, Fajardo was frequently in the Spanish Levante,[21] dedicating himself to dealing with the growing threat of Anglo-Barbary piracy in the Mediterranean, and trying to hunt down renowned pirates such as Zymen Danseker and Jack Ward.

He arrived at the Tunisian coast, where he attacked the fortified anchorage of La Goulette, destroying and capturing all the ships in the place,[23] which made clear the Spanish capacity to face the pirates.

[3] In 1612, some four galleys of Fajardo's fleet captured the French privateer Jehan Philippe de Castelane's ship, which was carrying the entire collection of manuscripts from the Zaydani Library, belonging to the Moroccan Sultan Muley Zidan.

[25] In August 1614, Fajardo commanded an expedition of almost 100 ships with 5,000 landing soldiers, with whom he conquered La Mamora, a military action that earned him great prestige for the measures he took during the attack, and for which he had no casualties.