He established the Tribunal del Consulado, a special court and administrative body for commercial affairs in the viceroyalty.

He also strengthened the navy and the artillery and gave a great impulse to mining in the district of Chucuito, thereby increasing the revenue of the government of the colony.

In 1617 he divided the government of Río de la Plata into two, Buenos Aires and Paraguay, both dependencies of the Viceroyalty of Peru.

Miguel de Cervantes included an appreciation of Borja y Aragón's works in his Viaje del Parnaso.

Francisco de Borja y Aragón married Anna Borgia d’Aragona e Pignatelli, Princess of Squillace.