Another transposition certainly took place on 14 June 1310 when the new chapel dedicated to St. Anthony at the left-hand end of the transept had been completed; the sacred remains were solemnly transferred.

On 14 February 1350, Cardinal Guido de Boulogne came to Padua to fulfil a vow (he had been cured of the black plague) and to give a precious reliquary in which St. Anthony's chin (or to be more precise his jawbone) was placed. A final, temporary transposition occurred at the beginning of the 16th century when St. Anthony's Gothic chapel was demolished to make room for the new Renaissance chapel, which, despite being incomplete, was inaugurated in 1532.