Sotomayor arrived in Chile in 1583 and found himself required to play the role of judge, hearing innumerable accusations against the previous governor Martín Ruiz de Gamboa.

Sotomayor wanted to extend the conquest of Chile in the style of Pedro de Valdivia, which is to say, by building a series of forts which would protect each other and the cities.

However, carrying out this project required a professional army, and requests for such were turned down by the Spanish authorities, due to the general scarcity of resources in the area and of the Crown.

He raised these forts with the goal of cutting communications among the Mapuches and hoped to quickly establish towns in each of these places, which would attract enough people to bring reinforcements to Chile persuaded that this was the best method of reducing the tribes for the definitive conquest.

Amidst these problems with the insurgency, Sotomayor also had to confront the attacks of English pirates, most notably Thomas Cavendish, who anchored in Quintero on April 9, 1587.

He left the old and circumspect lawyer Pedro de Viscarra, who had arrived from Spain two years earlier with the title of lieutenant governor of Chile.

In August, Sotomayor disembarked in Callao, where he learned that the king had named a new governor of Chile, Martín García Óñez de Loyola.