Having assembled about an hundred and fifty soldiers, Giron assumed the office of commander-in-chief of the army of liberty, appointing Diego de Alvarado the lawyer his lieutenant-general; Thomas Vasquez, Francisco Nunnez, and Rodrigo de Pineda captains of horse; the two last of whom accepted more from fear than affection. Juan de Pedrahita, Nuno Mendiola, and Diego Gavilan were made captains of foot; Albertos de Ordunna standard-bearer, and Antonio Carillo serjeant-major; all of whom were ordered to raise soldiers to complete their companies with every possible expedition. It being reported through the country that the whole citizens of Cuzco had concurred in this rebellion, the cities of Guamanga and Arequipa sent deputies to Cuzco, desiring to be admitted into the league, that they might jointly represent to his majesty the burdensome and oppressive nature of the ordinances imposed by the judges in relation to the services of the Indians. But when the citizens of Guamanga and Arequipa became rightly informed that this rebellion, instead of being the act of the Cabildo and all the inhabitants, had been brought about by the contrivance of a single individual, they changed their resolutions, and prepared to serve his majesty. About this time, the arch rebel Giron caused the deposed governor, Gil Ramirez, to betaken from prison and escorted forty leagues on his way towards Arequipa, and then set free.

Fifteen days after the commencement of the rebellion, finding himself at the head of a considerable force, he summoned a meeting of all the citizens remaining in Cuzco, at which there appeared twenty-five citizens who were lords of Indians, only three of whom were intitled from office to sit in that assembly. By this meeting, Giron caused himself to be elected procurator, captain-general, and chief-justice of Peru, with full power to govern and protect the whole kingdom both in war and peace. When news of this rebellion was brought to Lima by Hernando Chacon, who was foster-brother to Giron, the judges would not credit the intelligence, believing it only a false report, to try how the people stood affected to the cause, and therefore ordered Chacon to be imprisoned; but learning the truth soon afterwards, he was set at liberty, and the judges began seriously to provide for suppressing the rebellion, appointing officers and commanders to raise forces for that purpose. They accordingly sent a commission to Alonzo de Alvarado, then at La Plata, constituting him captain-general of the royal army against Giron, with unlimited power to use the public treasure, and to borrow money for the service of the war in case the exchequer should fail to supply sufficient for the purpose. Alvarado accordingly appointed such officers as he thought proper to serve under him, and gave orders to raise men, and to provide arms and ammunition for the war.

Besides the army which they authorized Alvarado to raise and command in Las Charcas, the judges thought it necessary to raise another army at Lima, of which Santillan, one of themselves and the archbishop of Lima were appointed conjunct generals. Orders were likewise transmitted to all the cities, commanding all loyal subjects to take up arms in the service of his majesty, and a general pardon was proclaimed to all who had been engaged in the late rebellions, under Gonzalo Pizarro, Don Sebastian de Castilla, and others, provided they joined the royal army within a certain given time. They likewise suspended the execution of the decrees for freeing the Indians from personal services, during two years, and repealed several other regulations which had given great and general offence to the soldiers and inhabitants, and had been the cause of all the commotions and rebellions which distracted the kingdom for so long a time.

While these measures were carrying on against him, Hernandez, Giron was not negligent of his own concerns. He sent off officers with detachments of troops to Arequipa and Guamanga, to induce the inhabitants of these cities to join him, and requiring them by solemn acts of their cabildos to confirm and acknowledge him in the offices he had usurped. He caused the cabildo of Cuzco to write letters to the other cities of Peru to concur in his elevation and to give assistance in the cause, and wrote many letters himself to various individuals in Las Charcas and other places, soliciting them to join him. Having collected an army of above four hundred men, besides the detachments sent to Guamanga and Arequipa, he resolved to march for Lima, to give battle to the army of the judges, as he called it, pretending that his own was the royal army, and that he acted in the service of his majesty. At the first he was undetermined, whether it might not be better to march previously against Alvarado, whose party he considered to be the weakest, owing to the great and cruel severity which that officer had exerted against the adherents of the late rebellions: And many judicious persons are of opinion that he would have succeeded better if he had first attacked the marshal, as in all probability he would have got possession of these provinces, and his men would not have deserted from him to a person so universally disliked for his cruelty, as they afterwards did when they marched towards Lima. He accordingly marched from Cuzco and crossed the river Apurimac; immediately after which Juan Vera de Mendoza and five others deserted from him, re-crossed the bridge, which they burnt to prevent pursuit, and returned to Cuzco, where they persuaded about forty of the inhabitants to set out for Las Charcas to join the marshal Alvarado.

At this time Sancho Duarte who was governor of the city of La Paz, raised above two hundred men in the service of his majesty, which he divided into two companies, one of horse and the other of foot. Giving the command of his infantry to Martin d'Olmos, he took the command of the horse himself, and assumed the title of general. With this force he set out for Cuzco, intending to march against Giron, but not to join the marshal Alvarado that he might not submit to his superior command. On his arrival at the bridge over the Rio Desaguadero, he learnt that Giron had left Cuzco to attack Lima, and proposed to have continued his march for Cuzco remaining independent of the marshal. But, in consequence of peremptory commands from Alvarado as captain-general, who highly disapproved of so many small armies acting separately, he returned to his own province.

Pursuing his march for Lima, Hernandez Giron learnt at Andahuaylas that the citizens of Guamanga had declared for his majesty, at which circumstance he was much disappointed. He proceeded however to the river Villca46, where his scouts and those of the royal army encountered. He proceeded however to the city of Guamanga, whence he sent orders to Thomas Vasquez to rejoin him from Arequipa. Although the inhabitants of that place, as formerly mentioned, had written to those of Cuzco offering to unite in the insurrection, supposing it the general sense of the principal people; they were now ashamed of their conduct, when they found the rebellion only proceeded from a few desperate men, and declared for the king; so that Vasquez was obliged to return without success. Being now at the head of above seven hundred men, though disappointed in his expectations of being joined by the citizens of Guamanga and Arequipa, Hernandez Giron pursued his march for the valley of Jauja; during which march Salvador de Lozana, one of his officers, who was detached with forty men to scour the country, was made prisoner along with all his party by a detachment from the army of the judges.

Notwithstanding this unforseen misfortune, Giron continued his march to the valley of Pachacamac, only four leagues from Lima, where it was resolved in a council of war to endeavour to surprise the camp of the royalists near the capital. Intelligence of this was conveyed to the judges, who put themselves in a posture of defence. Their army at this time consisted of 300 cavalry, 600 musqueteers, and about 450 men armed with pikes, or 1350 in all. It may be proper to remark in this place, that, to secure the loyalty of the soldiers and inhabitants, the judges had proclaimed a suspension of the obnoxious edicts by which the Indians were exempted from personal services, and the Spaniards were forbidden to make use of them to carry their baggage on journeys; and had agreed to send two procurators or deputies to implore redress from his majesty from these burdensome regulations.