The church was severely damaged in the Great Fire of 1212.
Rebuilding took place during the thirteenth century, although the exact dates are unknown.
In its reconstructed state – the basic layout of which survives today – the church was cruciform in plan, with an aisled nave of six bays, a crossing tower, transepts, and a five bay choir.
Beyond the choir stood a lower retrochoir or Lady chapel, the form of which can also be interpreted as group of four chapels with separate gabled roofs, two opening from the choir, and two from each aisle.

There was a chapel dedicated to Mary Magdalen, for the use of the parishioners, in the angle between the south transept and the choir, and another chapel was later added to the east of the retrochoir.
This was to become known as the "Bishop's chapel" as it was the burial place of Lancelot Andrewes.

In the 1390s, the church was again damaged by fire, and in around 1420 the Bishop of Winchester, Henry Beaufort, assisted with the rebuilding of the south transept and the completion of the tower.

During the 15th century the parochial chapel was rebuilt, and the nave and north transept were given wooden vaults following the collapse of the stone ceiling in 1469.
Some of the carved bosses from the vault (destroyed in the 19th century) are preserved in the cathedral.

The 14th-century poet John Gower lived in the priory precinct and is entombed in the church, with a splendid memorial, with polychrome panels.
There is also a recumbent effigy of a knight in timber (rather than brass or stone) and it is suggested by the church that this dates from the 13th century.
If so then this is one of the oldest such memorials and some credence can be given to the suggestion by its lack of heraldic emblems.
The church was severely damaged in the Great Fire of 1212. Rebuilding took place during the thirteenth century, although the exact dates are unknown. In its reconstructed state – the basic layout of which survives today – the church was cruciform in plan, with an aisled nave of six bays, a crossing tower, transepts, and a five bay choir. Beyond the choir stood a lower retrochoir or Lady chapel, the form of which can also be interpreted as group of four chapels with separate gabled roofs, two opening from the choir, and two from each aisle.
There was a chapel dedicated to Mary Magdalen, for the use of the parishioners, in the angle between the south transept and the choir, and another chapel was later added to the east of the retrochoir. This was to become known as the "Bishop's chapel" as it was the burial place of Lancelot Andrewes.
In the 1390s, the church was again damaged by fire, and in around 1420 the Bishop of Winchester, Henry Beaufort, assisted with the rebuilding of the south transept and the completion of the tower.
During the 15th century the parochial chapel was rebuilt, and the nave and north transept were given wooden vaults following the collapse of the stone ceiling in 1469. Some of the carved bosses from the vault (destroyed in the 19th century) are preserved in the cathedral.
The 14th-century poet John Gower lived in the priory precinct and is entombed in the church, with a splendid memorial, with polychrome panels. There is also a recumbent effigy of a knight in timber (rather than brass or stone) and it is suggested by the church that this dates from the 13th century. If so then this is one of the oldest such memorials and some credence can be given to the suggestion by its lack of heraldic emblems.
Southwark Cathedral