The expedition was deemed a great success and Ovando appointed Ponce de León governor of San Juan Bautista. This appointment was later confirmed by Ferdinand II on 14 August, 1509. He was instructed to extend the settlement of the island and continue mining for gold. The new governor returned to the island as instructed, bringing with him his wife and children.
Even as Ponce de León was settling the island of San Juan, significant changes were taking place in the politics and government of the Spanish West Indies. On 10 July, 1509, Diego Colón, the son of Christopher Columbus, arrived in Hispaniola as acting Viceroy, replacing Nicolás de Ovando. For several years Diego Colón had been waging a legal battle over his rights to inherit the titles and privileges granted to his father. The Crown regretted the sweeping powers that had been granted to Columbus and his heirs and sought to establish more direct control in the New World. In spite of the Crown's opposition, Colón prevailed in court and Ferdinand was required to appoint him Viceroy. Although the courts had ordered that Ponce de León should remain in office, Colón circumvented this directive on 28 October, 1509 by appointing Juan Ceron chief justice and Miguel Diaz chief constable of the island, effectively overriding the authority of the governor. This situation prevailed until 2 March, 1510, when Ferdinand issued orders reaffirming Ponce de León's position as governor. Ponce de León then had Ceron and Diaz arrested and sent back to Spain.