In his preface, Prescott explains his work: "I have accumulated a large amount of manuscripts, of the most various character, and from the most authentic sources." In addition to accessing primary sources including royal documents, personal diaries, and various private correspondences, Prescott also relied on several other scholars. Ultimately, he had more information on Peru than he did on his book for Mexico: "There is scarcely a nook or corner so obscure, in the path of the adventurer, that some light has not been thrown on it by the written correspondence of the period."
Progress on the book did not come easily. He found frequent inconsistencies or contradictions in his research and often had to determine how reliable his sources were. Further, he was frequently ill and was at first unable to work much. He used a bet with a friend to motivate him to write quickly but he was always hampered by his disability — Prescott was nearly blind. If he had tried to keep the fact a secret, the success of his previous works exposed it. The rumors were enough that he needed to address them directly in his preface: "I may be permitted to add a few [remarks] of a personal nature," he wrote. He had damaged his eyes while a student at Harvard, losing the vision in one of them completely, while the other was frequently useless as well. He would not call himself blind, nor would he allow his lack of vision to hamper him, however: "I resolved to make the ear, if possible, do the work of the eye."
Prescott hired a secretary, who read aloud to him the various materials he had gathered and wrote down any notes. Both his research and his notes upon them were read to him often enough that he memorized their contents — a staggering accomplishment considering the abundance of material. When alone, Prescott also utilized a "writing-case" (visible in the picture above) which guided his pen when he wanted to write himself. When his one working eye was well enough, he read as much as he could, possibly damaging it further, though it would inevitably fail after about an hour. In fact, Prescott surmised that the task of writing The History of the Conquest of Peru made him completely blind:
I have not had the use of it, on an average, for more than an hour a day. Nor can I cheer myself with the delusive expectation, that, impaired as the organ has become, from having been tasked, probably, beyond its strength, it can ever renew its youth, or be of much service to me hereafter in my literary researches.