He was present at the foundation of Santiago in 1541, he occupied various positions in the government of the city, and he was called on to defend it from the assault of Michimalonco cacique in September of the same year.

[1] Soon after assuming his post he discovered a conspiracy directed by Pedro Sánchez de la Hoz, that already had tried to seize the government on previous occasions, but that Valdivia had pardoned because of his possible influence in court.

This death caused problems for Valdivia, a judgment against him was made for various irregularities, but he overcame them, bringing in addition the designation of governor of Chile from the viceroy.

Villagra tried to stop the indigenous rebellion, led by Lautaro, but when facing him in the Battle of Marihueñu on 26 February he suffered a terrible defeat, having half of his soldiers killed and the remainder unable to prevent the destruction of Concepción.

The conflict was finally resolved when a petition was sent to the Audiencia in Lima,[3] which determined that the council had to submit to the command for six months, after which the viceroy Andrés Hurtado de Mendoza would designate a new governor.

The Governor then marched to the south, managed to reinforce the beleaguered cites there and then returned to surprise and defeat the Mapuches and kill Lautaro, in the Battle of Mataquito.

When initiating his rule he reorganized the regulation of the work in the mines and annulled the encomiendas that Garcia Hurtado de Mendoza had given to his friends and companions, which began new protests against him.

He also suffered in addition the death of his son Pedro de Villagra, el mozo in this war, which made his mental and physical condition worse.