In 1606, Fernandes was approached by the dignitaries of the cathedral of Puebla, inviting him to become the successor of his recently deceased friend Pedro Bermúdez as chapel master.
These manuscripts contain music by Spanish composers Francisco Guerrero, Cristóbal de Morales, and Pedro Bermúdez; the latter was with Fernandes at the time in the cathedral of Guatemala.
To complete these books, Fernandes composed a cycle of 8 Benedicamus Domino, the versicle that follows the Magnificat at vespers and certain Masses, one in each of the 8 ecclesiastical tones or modes.
During his Puebla tenure, rather than focusing on the composition of Latin liturgical music, he contributed a sizable amount of vernacular villancicos for matins.
This part of his output shows great variety in the handling of texts, which are in Spanish but also in pseudo-African dialects and Amerindian languages and occasionally Portuguese.