The Saint was buried in Padua on Tuesday 17 June, in the church of Santa Maria Mater Domini, which had been his spiritual refuge during the period of his most intense apostolic work. At the end of the funeral celebrations, St. Anthony's body was buried in the small church of the city's Franciscan friary. It was probably not placed underground, but left suspended in an ark-tomb so that the growing number of faithful could see and touch it.

The most important recognition and transposition took place on 8 April 1263. After a significant part of the construction of the new church had been completed, it was decided to transfer St. Anthony's body.

St. Bonaventure of Bagnoregio, who was then Minister General of the Franciscans, presided over the ceremony..

While examining the holy remains, before they were placed in a new wooden chest, he realised that St. Anthony's tongue was incorrupt.

Bonaventure exclaimed:
"O blessed tongue, which always blessed the Lord and made others bless him, now you show all the great merits you have acquired with God".

On that occasion, the tomb with St. Anthony's mortal remains was probably set in the centre of the transept, under the present conical cupola (the Angel cupola), in front of the presbytery.