He was minister of the Council of the Indies and of the Real Junta de Guerra de las Indias (Royal War Council of the Indies). He also served as captain general of New Spain during his term as viceroy.
He arrived in Chapultepec November 5, 1688 and took the oath of office on November 16. His formal entry into Mexico City took place on November 30, 1688 and his term of office is dated from that day.
The following month three English pirates arrived in the city under heavy guard. They had been taken prisoner at the Laguna de Términos, stating that they had been among a group of 100 English who had arrived seven months earlier to cut precious woods to be sent to Jamaica. The viceroy took steps to expel them.
The two brigantines returned, bringing news that they had found a few small ships and a half-built fort at San Bernardo Bay, Texas, but that the builders of the fort had been killed by Indians.
He ordered the construction of another aqueduct for Mexico City. This aqueduct ran from Alberca Chica of Chapultepec, at the foot of the hill, along the boulevards of Tacubaya and Arcos de Belén to a point in the city given the name El Salto del Agua (The Waterfall, literally Water Jump). This work, 3,908 meters long with 904 masonry arches was finally finished in 1779, during the term of Viceroy Antonio María Bucareli y Ursúa. Portocarrero bore the cost from his own pocket.
Fearing the presence of the French in San Bernardo and Espíritu Santo, Portocarrero accelerated the pacification of the province of Nueva Extremadura de Coahuila and named Captain Alonso de León governor. On August 12, 1689, de León founded the city of Santiago de la Monclova, named for the viceroy. One hundred fifty families were established there, including 270 well-armed men to repulse any incursions of the French. The viceroy also ordered the repair or construction of other forts farther north, all in communication with each other.
The viceroy ordered increased vigilance along the Gulf coast beyond Tampico, to guard against the forces of René-Robert Cavelier, Sieur de La Salle, marauding from Fort St. Louis in Matagorda (Texas). He expelled all foreign priests without licenses to preach in the colony.