Francisco de Ayeta (dates unknown) was a Spanish Franciscan missionary of the 17th century, in New Spain.

Francisco de Ayeta, missionary, was born in Pamplona, Spain, in 1640.

He entered the Franciscan order at the age of nineteen, he became successively Visitor of the Province of the Holy Evangel of New Mexico, and its Procurator at Madrid as well as Commissary of the Inquisition in New Spain.

Ayeta investigated remote missions personally, especially those of New Mexico, and he was the first to warn the Spanish authorities of the incipient Pueblo revolt.

His report, from 1678, induced the authorities of New Spain to reinforce the garrison at Santa Fe, but it was too late.