Navarrete was born in Castrogeriz, Spain, and became a Dominican in 1635. A graduate of and later lecturer in the celebrated San Gregorio College (Valladolid), Navarrete volunteered for the Asian Dominican missions in 1645. After ten years in the Philippines, he moved to China and worked in Fukien (Fujian) and Chekiang (Zhejiang), 1658-1666. He took a prominent part in the Chinese Rites Controversy, opposing the Jesuits, who argued that certain controversial rites should be tolerated in order to facilitate conversions.
Imprisoned from 1666 to 1670 in Canton (Guangzhou), he finally managed to return to Europe to present his case and prepare a trilogy on the mission's problems. His first book, Tratados (1676), includes a lively account of his travels in America and Asia (including India); his second, the more theological and polemical Controversias, was denounced by the Jesuits while still in press and was never published, though five truncated copies exist in libraries.
After 1677 his writing plans were frustrated by his promotion to the archbishopric of Santo Domingo (West Indies), where he died after a decade working for the welfare of the colony, particularly of its slave population. His Tratados, a monument of missionary and travel literature, was read by Locke, Quesnay and Voltaire, among others. It made a unique Spanish contribution to eighteenth-century Sinophilism.