It is assumed that the Magdalen Chapel was the starting-point of the work carried out by Giotto and his assistants in other parts of the Lower Church, including the right transept and the vault. It has been recently demonstrated that these areas were frescoed before Pietro Lorenzetti painted the scenes of the Passion in the left transept, a work executed before 1320. It is thought that as soon as the frescoes in the Magdalen Chapel were completed, Giotto and his workshop were commissioned to redecorate the right transept of the vault. This area had been previously frescoed in the late thirteenth century, as is indicated by the presence of Cimabue's large fresco of the Madonna enthroned with angels and St. Francis, which was spared.
At the beginning and in the middle of the 20th century the frescoes in the Lower church were cleaned and painstakingly restored. Since then some have held them to be the work of utmost quality from Giotto's own hand, others as the ambitious work of pupils. The debate is open up to now.