The licentiate Alvarez always accompanied the viceroy, and these two established themselves as the court of royal audience, in virtue of a commission from his majesty which the viceroy still held. By this royal order, the viceroy was authorised after his arrival at Lima, to hold audience in conjunction with two or one of the oydors who might first arrive, or even in case that any two or three of them should chance to die. In pursuance of this authority, the viceroy ordered a new seal to be made, which he committed to the custody of Juan de Leon, alcalde or police judge of Lima, who had been nominated by the Marquis of Camarosa, grand-chancellor of the Indies, as his deputy or chancellor of the audience of Lima. De Leon had fled from Gonzalo Pizarro, and had joined the viceroy at Quito. In consequence of this arrangement, the viceroy issued such orders and proclamations as seemed needful or expedient, in the name of the emperor Don Carlos; authenticating them with the royal seal, and by the signatures of himself and the licentiate Alvarez. By these means there were two royal audiences in Peru, one at the city of Lima, and the other wherever the viceroy happened to reside; so that it frequently happened that two opposite and contradictory decrees were pronounced and promulgated, in one and the same cause.

On taking the resolution of marching from Quito, the viceroy sent his brother-in-law, Diego Alvarez de Cueto, to inform his majesty of the state of affairs, and to solicit such reinforcements as might enable him to re-establish his authority in Peru, by waging war against Gonzalo Pizarro. Cueto went accordingly to Spain in the same fleet with Vaca de Castro and Texada, as already related. The viceroy advanced southwards to San Miguel, which is an hundred and fifty leagues from Quito, determining to remain at that place till he might receive farther orders from his majesty. The inhabitants of San Miguel gave him the best reception in their power, and furnished him as far as they were able with every thing he was in want of. He continually kept his small army on foot, to preserve the honour and reputation of his character as viceroy, and that he might be in a convenient situation for receiving such reinforcements as might come from Spain or from any of the American colonies; as every one coming by land from these quarters must necessarily pass by the way of San Miguel, especially if accompanied by horses or beasts of burthen. He expected therefore to be able in this place to collect reinforcements to his army, so as to be in condition to renew the war, and employed himself to collect men, horses, and arms, so that he was soon at the head of five hundred men, tolerably equipped. Some of these indeed were in want of defensive armour, which they endeavoured to supply by fabricating cuirasses of iron, and of hard leather.

At the time when Gonzalo Pizarro sent Bachicao with the brigantines to get possession of the ships belonging to the viceroy, he dispatched Gonzalo Diaz de Pinera and Jerom de Villegas to collect the soldiers who dwelt in Truxillo and San Miguel, that they might make head against the viceroy in the north of Peru. These officers remained in San Miguel with about eighty men whom they had drawn to their party, till they heard of the approach of the viceroy; on which, not being in sufficient force to oppose him, they retreated towards Truxillo, and established themselves in the province of Collique, about forty leagues14 from San Miguel. From thence they sent intimation to Gonzalo of the advance of the viceroy, and that his army increased daily in numbers, insomuch that it behoved him to think of some appropriate measures to avert the threatened danger. Diaz and Villegas were likewise informed that the viceroy had sent Juan de Pereira, one of his officers, into the province of Chachapoyas, in which there were very few Spanish settlers, to endeavour to collect reinforcements. As they believed that Pereira and his followers entertained no suspicions of their being in the neighbourhood, Diaz and Villegas determined on attempting to surprize them, which they did so effectually one night, that they made the whole party prisoners without resistance. Having beheaded Pereira and two of his principal followers, they obliged the rest of the party, about sixty horsemen, to enter into the service of Gonzalo, by threats of putting them all to death if they refused; after which they returned to their post.

The viceroy was greatly incensed by this untoward event, and determined to seek an opportunity of revenge. With this view he departed secretly from San Miguel with a body of an hundred and fifty horse, and took such judicious measures that he arrived one night undiscovered at Collique, where he surprized the enemy, and obliged them to fly in all directions. Diaz made his escape almost alone into a district inhabited by hostile Indians, who assailed him and put him to death. Villegas and Ferdinand Alvarado were more fortunate in their escape, as they were able to collect some of their dispersed troops, with whom they took up a new and more secure position not far from Truxillo, and at a safer distance from San Miguel.

As Gonzalo Pizarro was informed that the viceroy augmented his army from time to time, more especially after this successful enterprize, he resolved to march against him without delay; as hardly a day passed in which the viceroy was not joined by soldiers, horses, and arms from Spain, or some of the American colonies, all of which were landed at the port of Tumbez. He was likewise in dread lest some dispatch might arrive from the emperor, favourable to the viceroy, by which his own adherents might be intimidated, and numbers might be induced to change sides. With this view he assembled his army, determined to march in person against the viceroy, and if possible to bring him to action. He issued therefore the proper orders to all his officers, reviewed and mustered his troops, advanced them the necessary funds for taking the field, and sent off the baggage, artillery, ammunition and provisions, with the main body of the army towards Truxillo, remaining behind at Lima with some of his principal officers, to follow in proper time. About this time a vessel arrived from Arequipa with a very seasonable supply of 100,000 crowns; and another vessel from Tierra Firma, belonging to Gonzalo Martel, sent by his wife to enable him to return home. The arrival of these two vessels was very opportune for Gonzalo Pizarro, as they served to transport great quantities of musquets, pikes, ammunition, and other implements of war, together with a guard of an hundred and fifty men, and greatly facilitated the intended expedition against the viceroy.

On quitting Lima, Gonzalo Pizarro thought proper to take the oydor Cepeda and Juan de Caceres the accountant-general along with him, both to give the more eclat and appearance of legal authority to his measures, and on purpose to break up the court of royal audience, as Ortiz de Zarate would then be the only judge remaining at Lima, who was not thought of much importance, as he was in bad health. Besides, Blas de Soto, his brother, had married the daughter of that judge; and although that marriage had been effected contrary to the wish of Ortiz, it was considered as some tie upon his conduct. For greater security, however, Gonzalo used the precaution of carrying the royal seal along with him. Gonzalo Pizarro chose to go by sea; and on leaving Lima, he appointed Lorenzo de Aldana as lieutenant-governor of that city, with a garrison of eighty soldiers, to preserve tranquillity during his absence. This small number was considered sufficient to prevent any attempt towards a revolutionary movement, as most of the inhabitants of Lima accompanied the expedition. Gonzalo embarked in March 1545, and landed at the port of Santa, fifteen leagues south from Truxillo, at which city he arrived on Palm Sunday. He remained at this place for some time, waiting the junction of his troops, sending messages in various directions to expedite their march. After some time, he marched from Truxillo into the province of Collique, where the whole of his army assembled. At this place he reviewed his army, which amounted to above six hundred horse and foot. The troops under the viceroy were nearly as numerous; but those under Gonzalo were much better armed, and better supplied with every thing requisite for war, as well as being all veteran soldiers, accustomed to war and discipline, and well acquainted with all the difficult passes of the country. The troops of the viceroy on the contrary, had for the most part come recently from Spain, were quite unaccustomed to war, and ill armed; besides which their powder was bad in quality.