Having thus reduced the affairs of the kingdom to good order, all the unemployed soldiers being sent off to different places, some to Chili, others to the new province on the Rio Plata, and others to various new discoveries under different commanders, and all who remained in Peru being established in various occupations by which they might maintain themselves, according to their inclinations and capacities, mostly in the concerns of the mines, the president resolved to return, into Spain, pursuant to the authority he had received from his majesty to do so when he might see proper. One of his most powerful motives for returning to Spain proceeded from his anxiety to preserve the large treasure he had amassed for the king: as, having no military force for its protection, he was afraid such great riches might excite fresh troubles and commotions in the country. Having made all the necessary preparations for his voyage, and embarked his treasure, without communicating his intentions hitherto to any one, he assembled the magistrates of Lima, and informed them of his intended voyage. They started many objections to this measure; representing the inconveniencies which might arise from his departure, before his majesty had sent out some other person to replace him, either in the capacity of viceroy or president. He answered all their objections, stating that the court of royal audience, and the governors of the different provinces which they were authorized to nominate, were sufficient to dispense justice and to regulate all affairs, they at last consented; and immediately embarking, he set sail for Panama.
Just before he sailed and while on board ship, the president made a new partition of such lands and Indians as had become vacant since the former distribution which he made at Cuzco. The number of vacant repartimientos was considerable, in consequence of the death of Centeno, De Royas, the licentiate Carvajal, and several other persons of rank; and as there were many candidates who demanded loudly to be preferred, he chose to defer the repartition till after he had embarked, as he was unable to satisfy all the claimants, and was unwilling to expose himself to the clamours of those whom he was unable to gratify. Having settled all these distributions, he left the different deeds signed and sealed with the secretary of the royal audience, with strict injunctions that they should not be opened until eight days after his departure. Every thing being finally concluded, he set sail from the port of Callao in December 1549, accompanied by the Provincial of the Dominicans and Jerom de Aliaga, who were appointed agents for the affairs of Peru at the court of Spain. He was likewise accompanied by several gentlemen and other considerable persons, who meant to return to Spain, carrying with them all the wealth they had been able to acquire.