While in prison and till his death, Centeno, to whose custody he had been committed, treated him with much civility, and would not allow any one to insult his fallen greatness. When about to be put to death, Gonzalo made a gift of the magnificent dress which he then wore to the executioner; but Centeno paid its full value to the executioner, that the body might not be stripped and exposed till carried away for interment; and next day he had it carried to Cuzco and respectfully buried. But the head, pursuant to the sentence, was carried to Lima.

On the same day in which Pizarro was beheaded, his lieutenant-general Carvajal was drawn and quartered, and eight or nine of the insurgent captains were hanged; and in the sequel several others of the principal persons concerned in the revolt were punished when taken38. On the day following the president went to Cuzco with all his army, whence he sent Alfonzo de Mendoza with a detachment into Las Charcas, to make prisoners of those who had been sent into that district by Gonzalo in quest of silver, and such as might have fled thither from the battle. On account of the rich mines in the province of Las Charcas, especially Potosi, it was supposed that many of the fugitives had taken refuge in that place, to which Hondegardo was sent as lieutenant-governor and captain-general, with orders to chastise all those of the inhabitants who had been guilty either of favouring Gonzalo, or of neglecting to repair to the royal standard on the summons of the president. Along with Hondegardo, Gabriel de Royas was sent as receiver of the royal fifth and other tributes belonging to the king, and of the fines which the governor might inflict on the disaffected and recusants. As De Royas soon died, Hondegardo had to discharge the united functions of governor and receiver of the province, and in a short space of time he amassed treasure to the amount of 3,600,000 livres39, which he transmitted to the president.

The president remained for some time at Guzco, occupied in punishing the insurgents according to the greatness of their crimes. Those whom he deemed most guilty, he condemned to be drawn in pieces by four horses, others he ordered to be hanged; some to be whipt, and others were sent to the galleys. He applied himself likewise with much attention to restore the kingdom to good order. In virtue of the authority confided to him by the king, he granted pardons to all who, having been in arms in the valley of Xaquixaguana, had abandoned Gonzalo and joined the royal standard. These pardons referred to all public crimes of which they had been guilty during the rebellion of Gonzalo Pizarro, yet leaving them liable to answer in civil actions for every thing respecting their conduct to individuals. This battle of Xaquixaguana, which will be long famous in Peru, was fought on Monday the 9th of April 1548.

When the president had dispatched the most urgent affairs connected with the suppression of the rebellion, there yet remained an object of great importance for the quiet of the kingdom, which was surrounded with many difficulties. This was with regard to the dismissal of the army, in such a manner that so great a number of soldiers set free from the restraints of discipline might not occasion troubles similar to those now put an end to. On purpose to succeed in this delicate affair, the utmost prudence was requisite, as almost every soldier in the army considered himself entitled to one of the best of the vacant repartimientos, and as the number of the troops exceeded 2500 men, while there were only 150 repartimientos to distribute. Hence it was quite obvious, that instead of being able to gratify every claimant, far the greater part must be dissatisfied. After a serious deliberation on this important subject, the president went to a place in the province of Apurimac, about twelve leagues from Cuzco, accompanied only by the archbishop and one secretary, on purpose to have leisure for mature reflection at a distance from the perpetual importunities of the claimants. In this place, they made the best distribution in their power of the vacant repartitions, giving sufficient means of living in a respectable manner to the captains and other persons of consideration, each in proportion to their respective merits and the services they had been of in suppressing the late rebellion, giving new repartitions to those who had none, and increasing those of others. On this occasion it was found that they had vacant repartitions to distribute to the value of a million of gold crowns in yearly rent. The greater number of the most valuable and extensive repartitions had become vacant during the troubles, partly from their former possessors having been put to death by Gonzalo, either under pretence of guilt in opposing his rebellion, or in the various engagements during the troubles. The president had likewise capitally punished several to whom Gonzalo had given repartitions. It must however be remarked, that several of these most valuable repartimientos had been retained by Gonzalo for his own benefit, under pretence of providing for the expences of the war.

In making the new grants, the president retained the power of granting pensions upon some of the most extensive repartitions, of three or four thousand ducats from each, more or less according to their respective values, on purpose to have the power of dividing the money among such soldiers as he could not otherwise reward, to enable them to procure arms, horses, and other necessaries, meaning to send them off in various directions to discover and subdue the country which was hitherto unoccupied. Having thus regulated every thing to the best of his power, the president thought proper to retire to Lima, and sent the archbishop to Cuzco to publish the regulations and distribution of repartimientos, and to make payment of the several rewards in money which had been agreed upon. The arrangement of this affair occasioned much dissatisfaction among the soldiers, every one believing himself better entitled to some allotments of lands and Indians than several of those who had acquired such grants. All the fair speeches and promises of the archbishop and the principal officers were insufficient to quiet the murmurs and discontents of the troops, which even produced some commotions and seditious conspiracies, in which it was proposed to seize upon the archbishop and the chief officers of the army and government, and to send the licentiate Cienca with a remonstrance to the president, demanding of him to recal the repartition which he had decreed, and to make a new one more favourable to their wishes. They even threatened to revolt, and to take possession by force of what they considered due to their services. The licentiate Cienca, who had been appointed chief justice at Cuzco, had established so excellent a system of police that he had immediate notice of all these plots and commotions, and was soon enabled to restore order and tranquillity by arresting and punishing the principal agitators of these threatened troubles, by which he effectually checked the spirit of mutiny and insubordination, and averted at least for the present the danger of a new civil war in the kingdom.

Before leaving Cuzco, the president had renewed the commission of Valdivia as governor of Chili, as a reward for the services he had rendered in the late war against Gonzalo. On purpose to provide the reinforcements of men, horses, and arms, which were necessary for defending and extending his conquests in that province, Valdivia went to Lima as the most convenient situation for procuring what he wanted. Having completed all his preparations, he embarked all his men and military stores at the port of Callao, and sent them off for Chili; but chose to go himself by land to Arequipa, where he proposed to take shipping in his way back to his government. A report was made to the president, that Valdivia had engaged some officers and soldiers from among those who had been sentenced to banishment from Peru, and even some of those who had been condemned to the galleys, on account of the share they had taken in the late rebellion. In consequence of this information, the president sent his lieutenant-general Hinojosa with orders to bring Valdivia before him to answer for his conduct in these things which were laid to his charge. As Valdivia was accompanied by a considerable number of men he believed himself in condition to resist this mandate, and refused the earnest solicitations of Hinojosa to go back along with him to the president. But, as Hinojosa observed that Valdivia took no precautions to prevent his arrest, and had no suspicions that any force would be used against him, he resolved to attempt to make him prisoner with the assistance only of six musqueteers, in which he succeeded without opposition. In this situation, Valdivia very properly determined to submit with a good grace, and so satisfactorily explained his conduct to the president, that he was allowed to resume his voyage, and to take all those people along with him whom he had engaged.