Two days after the arrival of Giron in the valley of Pachacamac, a party of his army went out to skirmish with the enemy, on which occasion Diego de Selva and four others of considerable reputation deserted to the judges. For several days afterwards his men continued to abandon him at every opportunity, twenty or thirty of them going over at a time to the royal army. Afraid that the greater part of his army might follow this example, Hernandez Giron found it necessary to retreat from the low country and to return to Cuzco, which he did in such haste that his soldiers left all their heavy baggage that they might not be encumbered in their march. On this alteration of affairs, the judges gave orders to Paulo de Meneses to pursue the rebels with six hundred select men; but the generals of the royal army would not allow of more than a hundred being detached on this service. During his retreat, Giron, finding himself not pursued by the royalists with any energy, marched with deliberation, but so many of his men left him that by the time he reached the valley of Chincha his force was reduced to about 500 men. Paulo de Meneses, having been reinforced, proposed to follow and harass the retreating rebels; but not having accurate intelligence, nor keeping sufficient guard, was surprised and defeated by Giron with some considerable loss, and obliged to retreat in great disorder. Yet Giron was under the necessity to discontinue the pursuit, as many of his men deserted to the royalists.

Sensible of the detriment suffered by the royal interests in consequence of the disagreement between the present generals, Judge Santillan and Archbishop Loyasa, to which the defeat of Meneses was obviously owing, these very unfit persons for military command were displaced, and Paulo de Meneses was invested in the office of commander-in-chief, with Pedro de Puertocarrero as his lieutenant-general. This new appointment occasioned great discontent in the army, that a person who had lost a battle, and rather merited ignominy and punishment for his misconduct, should be raised to the chief command. The appointment was however persisted in, and it was resolved to pursue the enemy with 800 men without baggage.

Hernandez Giron, who retreated by way of the plain towards Arequipa, had reached the valley of Nasca, about sixty leagues to the southwards of Lima, before the confusion and disputes in the royal camp admitted of proper measures being taken for pursuit. At this time, the judges gave permission to a sergeant in the royal army, who had formerly been in the conspiracy of Diego de Royas, to go into the enemys camp disguised as an Indian, under pretence of bringing them exact information of the state of affairs. But this man went immediately to Hernandez, whom he informed of the quarrels among the officers and the discontents in the royal army. He likewise informed him that the city of San Miguel de Piura had rebelled, and that one Pedro de Orosna was coming from the new kingdom of Grenada with a strong party to join the rebels in Peru. But to qualify this favourable news for the rebels, Giron received notice at the same time that the marshal Alvarado was coming against him from Las Charcas with a force of twelve hundred men. About this time, on purpose to reinforce his army, Giron raised a company of an hundred and fifty negroes, which he afterwards augmented to 450, regularly divided into companies, to which he appointed captains, and allowed them to elect their own ensigns, sergeants, and corporals, and to make their own colours.

In the mean time, the marshal Alonzo de Alvarado, employed himself diligently in Las Charcas to raise men for the royal service, and to provide arms, ammunition, provisions, horses, and mules, and every thing necessary for taking the field. He appointed Don Martin de Almendras, who had married his sister, lieutenant-general, Diego de Porras standard-bearer, and Diego de Villavicennio major-general. Pera Hernandez Paniagua, Juan Ortiz de Zarate, and Don Gabriel de Guzman, were captains of horse. The licentiate Polo, Diego de Almendras, Martin de Alarzon, Hernando Alvarez de Toledo, Juan Ramon, and Juan de Arreynaga, were captains of foot; Gomez Hernandez the lawyer, military alguazil or judge-advocate, and Juan Riba Martin commissary-general. His force amounted to 750 excellent soldiers, all well armed and richly clothed, with numerous attendants, such as had never been seen before in Peru. I saw them myself a few days after their arrival in Cuzco, when they made a most gallant appearance. While on his march to Cuzco from La Plata, Alvarado was joined by several parties of ten and twenty together, who came to join him in the service of his majesty. On his way to Arequipa he was joined by about forty more; and after passing that place, Sancho Duarte and Martin d'Olmos joined him from La Paz with more than two hundred good soldiers. Besides these, while in the province of Cuzco, he was joined by Juan de Saavedra with a squadron of eighty five men of the principal interest and fortune in the country. On entering Cuzco, Alvarado was above 1200 strong; having 300 horse, 350 musqueteers, and about 530 armed with pikes and halberts. Not knowing what was become of Giron, Alvarado issued orders to repair the bridges over the Apurimac and Abancay, intending to pass that way in quest of the rebels. But receiving intelligence from the judges, of the defeat of Meneses, and that the rebels were encamped in the valley of Nasca, he ordered the bridges to be destroyed, and marched by the nearest way for Nasca, by way of Parinacocha, in which route he had to cross a rocky desert of sixty leagues.

In this march four of the soldiers deserted and went over to Hernandez Giron at Nasca, to whom they gave an account of the great force with which Alvarado was marching against him, but reported in public that the royalists were inconsiderable in number. Giron, however, chose to let his soldiers know the truth, and addressed his army as follows. "Gentlemen, do not flatter or deceive yourselves: There are a thousand men coming against you from Lima, and twelve hundred from the mountains. But, with the help of God, if you stand firm, I have no doubt of defeating them all." Leaving Nasca, Giron marched by way of Lucanas, by the mountain road, intending to take post on the lake of Parinacocha before Alvarado might be able to reach that place. He accordingly left Nasca on the 8th of May47 for this purpose.

In the mean time pursuing his march, Alvarado and his army entered upon the desert of Parihuanacocha, where above sixty of his best horses died, in consequence of the bad and craggy roads, the unhealthiness of the climate, and continued tempestuous weather, though led by hand and well covered with clothes. When the two armies approached each other, Alvarado sent a detachment of an hundred and fifty select musqueteers to attack the camp of Giron, and marched forwards with the main body of his army to support that detachment. An engagement accordingly took place in rough and strong ground, encumbered with trees brushwood and rocks, in which the royalists could make no impression on the rebels, and were obliged to retire with the loss of forty of their best men killed or wounded. In the following night, Juan de Piedrahita endeavoured ineffectually to retaliate, by assailing the camp of Alvarado, and was obliged to retreat at daybreak. Receiving notice from a deserter that the rebel army consisted only of about four hundred men, in want of provisions, and most of them inclined to revolt from Giron and return to their duty, Alvarado determined upon giving battle, contrary to the opinion and earnest advice of all his principal officers and followers. But so strong was the position of the enemy, and the approaches so extremely difficult, that the royal army fell into confusion in the attack, and were easily defeated with considerable loss, and fled in all directions, many of them being slain by the Indians during their dispersed flight.