When Francis I's armies invaded Navarre in May of 1521, the local tribunal of the Inquisition fled west along the Ebro from Tudela to the nearest episcopal town, Calahorra, losing all of its prisoners and part of its records during the hasty exit. The diocese of Calahorra was immediately detached from the Valladolid Inquisition and transferred to Navarre. Barely a month later, the French reeled back in unexpected defeat, but the Holy Office continued to reside outside Navarre.

Both before and after the French invasion, the Cortes and Viceroy of Navarre had requested that the seat of their Inquisition be moved to Pamplona, capital of this small kingdom. In August 1521, the Supreme Council of the Inquisition laid down its rulings on the petitions of Navarre's Cortes. They agreed that all ordinary voting judges, the consultores and letrados, should be Navarrese, but categorically rejected the demand that Inquisitors should likewise be Navarrese.