He participated actively in many maritime explorations, which led to him being appointed by the Audiencia of Panama as a piloto mayor of the Mar del Sur (the Spanish name for the Pacific Ocean at the time).

This task was given by the Viceroy of Peru to Pastene, in 1543, for which he was awarded the title of general de la Mar del Sur.

In 1544 Pedro de Valdivia entrusted exploring the coasts of the south to Pastene, ordering him to reach the Strait of Magellan.

In 1550, Pastene supported Valdivia's campaign into Mapuche territory in what is now the Biobío Region linking up with the conquistadors land expedition at Penco with his two ships on February 23, 1550.

During the Government of García Hurtado de Mendoza, Juan Bautista Pastene made a naval reconnaissance down the coast to Chiloé.