In 1559, Philip II again appointed Menéndez as Captain General, and his brother Bartolomé Menéndez as Admiral, of the Fleet of the Indies. He sailed for the Indies that October as captain general and commanded the galleons of the great "Armada de la Carrera", or Spanish Treasure Fleet, on their return voyage from the Caribbean and Mexico to Spain. Menéndez determined the route they followed, which led through the Straits of Florida () and up the east coast of Florida, taking advantage of the current of the Gulf Stream. In 1561, however, Menéndez was jailed by Casa officials for alleged smuggling, but he got his case transferred to court and won his release.