In 1575, however, as a result of a dispute between the Real Audiencia and the governor at the time, Melchor Bravo de Saravia, he was called a second time to take charge of the Reino of Chile. He was sworn in that same year in front of the "cabildo". Quiroga's second administration was more turbulent then the first. In addition to the ongoing war of Arauco, there were incursions by pirates, two earthquakes (in 1575) and a dispute with the bishop of San Miguel over the naming of ecclesiastical posts and the reduction of the income of the clerics, which put him in danger of excommunication.