Interested in the ritual practices of the natives, Molina used to congregate elders and former Inca priests in his parish or in the villages he visited to learn about pre-Hispanic stories and beliefs.
[3] Between 1568 and 1571 Cristóbal de Albornoz, general ecclesiastical visitor in Arequipa, was sent to Huamanga (today Ayacucho) in the Peruvian highlands to identify and destroy idolatry (the shrines of the Natives) and to punish the persons and communities who worshipped them.
Because of his knowledge of ritual practices and of the native cultural and religious world, Molina and another Spanish clergy, Olivera, were required to collaborate with Albornoz in his fight against idolatry and against the Taki Unquy messianic movement, which broke out in the central Andes around 1564.
For this reason he had appointed Francisco de Toledo as viceroy in 1569 and charged him (among other tasks) with producing the proof that the Incas were tyrants, conquered their territories by subjugation of the local people and were not legitimate rulers.
[1] On 24 September 1572 the last Sapan Inca, Túpac Amaru, was executed in Cusco, and Molina was one of the priests who accompanied him to the central square where a black-draped scaffold had been erected.
The name of Molina appears again in January 1577 when he testified in Cusco at inquiries about the campaigns against idolatry by Cristóbal de Albornoz.
He was simply introduced as a clérigo presbítero (cleric priest), and witnessed that he had known Albornoz for more than ten years and that the latter had successfully completed his service against idolatry in Huamanga (today Ayacucho).
He brought with him a letter signed by the caciques principales (main local chiefs) of Cusco, who were requesting the Viceroy to exempt them from taxes.
In his work there is also a desire to fuse the classic oral stories of the Andean tradition with biblical writings, trying to blend them with a clearly catechetical purpose.
[3] Molina states at the very beginning of his work, referring to the bishop, that the Account was prepared with the aim to «…understand the origins of their idolatries, because it is true that these [Incas] did not use writing [but], they had in a House of the Sun … next to Cusco, [where] the life of each of the Incas, the lands that [each of them] conquered, and their origin [are] painted with figures on boards …» and, referring to the Bishop Lartaun, in order «that Your Most Reverend Lordship [can] learn about the ceremonies, rituals, and idolatries that these Indians had.
The latter is the most extensive part of information: it contains data on the periodic festivals of the Natives, particularly the Inti Raymi and Situa and includes also a valuable collections of prayers and songs in Quechua with their translation into Spanish.
The Peruvian historian and critic Raúl Porras Barrenechea defined Molina the great canonist of the Native American liturgy.