Don Diego had hardly got two leagues from Lima, in 1542, when secret orders arrived there from Vaca de Castro, addressed to F. Thomas de San Martin, provincial of the Dominicans, and Francisco de Barrionuevo, to whom he committed the direction of public affairs till his own arrival. By these persons, the cabildo of the city was secretly assembled in the Dominican convent, to whom these orders were communicated, and who immediately recognized Vaca de Castro as governor, and Geronimo de Aliaga, his principal secretary, as adelantado or lieutenant governor of Peru. Immediately upon this formal act of recognition, the members of the cabildo and several of the principal citizens fled to Truxillo, fearing the resentment of the Almagrians. Although all this had passed in secret, it was communicated on the same night to Don Diego, who was disposed in consequence to have returned with the intention of giving up the city to plunder; but he was afraid lest by delay Holguin might escape into the north of Peru, and lest by returning, the arrival of the new governor might come to the knowledge of his troops. He determined therefore to continue his march against Holguin with all expedition. In spite of all his precautions, intelligence of the arrival of the new governor reached his camp, on which several persons abandoned him secretly, particularly the provincial of the Dominicans, Diego de Aguero, Juan de Saavedra, Yllen Suarez de Carvajal the commissary, and Gomez de Alvarado.
Although every consideration prompted Don Diego to use the utmost diligence in the present posture of affairs, he was under the absolute necessity of marching slowly, as Juan de Herrada his great friend and adviser fell sick of a mortal distemper. Owing to this delay, Holguin was enabled to get beyond the valley of Jauja in his march towards the province of Chachapoyas. Yet Don Diego followed after him with so much diligence that he very nearly got up with him. In this emergency, as Holguin was by no means in sufficient force to venture a battle with Don Diego, he put the following stratagem in practice to enable him to escape, which effectually succeeded. During the night he detached twenty horsemen to make an attack on the advanced guard of the enemy, with orders to take some prisoners if possible, and then to retire. They executed their orders successfully and made three prisoners, two of whom Holguin ordered to be immediately hanged,