Gods of the Andes provides the first English translation of the earliest lengthy description of Inca religion, An Account of the Ancient Customs of the Natives of Peru (1594). The Account is part of a Jesuit tradition of ecumenical works on religion that encompasses the more famous writings of Matteo Ricci in China and Roberto de Nobili in India. It includes original descriptions of many different aspects of Inca religion, including human sacrifice, the use of hallucinogens, mummification rituals, the existence of transgendered priests in the ancient Andes, divination rituals based on animal entrails, oracles, burials, and confession.

In her introductory chapters, Sabine Hyland presents the controversial life of the ascribed author, Blas Valera, a Jesuit who was ultimately imprisoned and exiled by the Jesuits for his "heretical" belief that the Incas worshipped the same creator god the Christians did; examines the Account in the light of other colonial writings about the Incas; and outlines what we know about Inca religion through other sources, comparing Valera's version to those of other writers.