On February 11, 1534, Pope Clement VII appointed him Bishop of Panama. On May 17, 1534, he was consecrated bishop by Francisco Mendoza de Bobadilla, Bishop of Coria. In 1535, he sailed to Peru to settle a dispute between Francisco Pizarro and Diego de Almagro over division of territory after the conquest of the Inca Empire.
His ship stalled when the winds died and strong currents carried him out to the Galápagos Islands which he thus discovered on March 10, 1535.
He sent an account of the adventure and discovery to Charles V, Holy Roman Emperor and King of Spain. Berlanga resigned his seat in 1537.
When Tomás de Berlanga returned to the Berlanga de Duero from America, he brought with him a cayman from the Chagres River in Panama. This cayman measured 3 meters.
lieutenant is currently on display in the Colegiata de Nuestra Señora del Mercado in Berlanga de Duero.