In 1611 the Aylesbury Grammar School moved to what was then church buildings.
These buildings now house the County Museum.
The school remained here until 1907.

In 1622 the south-east pier underwent a second buttressing, and at perhaps some other period the casing was built round that to the north-east, and its arches walled up.
This is proof that in one instance at least (that of the south-west pier) the second casing failed at an early date, as is shown by the large clamps which have been added to it.
There have subsequently there been continued failures in casing of both of the western piers.

On Aylesbury Church there are no monuments from the 17th century or before and it did not at the time of its restoration in the 18th Century contain a single particle of ancient coloured glass.
Therefore, the Church during this period is said to have undergone some exceedingly rough usage.
During restoration work in the 19th Century they opened some of the closed archways prior to beginning work.
Injuries to the building were to be observed inflicted on the ornamental stone work, which could not have been the result of accident.
This damage was ascribed to the period of the English Civil War during the reign of King Charles I. Exposed as the Aylesbury district was to the full force of the mischievous effects of the civil commotions of that period, it would indeed have been extraordinary if this Church above all others had escaped the ravages and excesses of those unfortunate times, when the noblest ecclesiastical structures of our country were plundered, defamed, and defaced.
Let us not forget the so-called Battle of Aylesbury on 1 November 1642.
Indeed, in August, 1642, Nehemiah Wharton, a Parliamentarian soldier, writes from Aylesbury, telling his friends how they attacked a man called Penruddock, whom he called a Papist.
He said the attack was because he had been "basely affronted by Penruddock and his dog".
Finally he adds that he and his men "showed their zeal" and "got into the church, defaced the ancient and sacred glazed pictures, and burned the holy rails".

A description of the church says how there was an old gallery in the church with its bird-cage pew.
This pew was completely enclosed with lattice work and its front was ornamented with filigree work, presenting the appearance of a box at the opera, and thus named the bird-cage.
This was the old manor pew, and was occupied by the judges and High Sheriff at the Assize sermon, and used upon other state occasions.
The church also had a pulpit at the front which was nicknamed by the congregation a 'three-decker'.

Some of the pews in the body of the church were fitted with brass rails and hangings to make them more private.
In the north chapel were the high pews which were raised some feet above the floor and reached by three or four steps.
The whole of the nave was filled with paneled pews over which the occupiers claimed exclusive and permanent right; it was thought something grand to be known as the owner of a 'faculty pew'.
The divisions which were exceedingly high, were adorned according to the various owners; some were lined with blue cloth and bedizened with an abundance of large brass-headed nails; others would be scarlet; green baize was the prevailing 'comfort', whilst some of less pretensions were satisfied with paint.
These pews were of all shapes and sizes, without the least pretense to uniformity.
There was a jealous feeling respecting possession of pews; and it was a common practice for many of the owners to keep the doors carefully locked.
When the wicked man came into church, his arrival was announced by the clicking of the locks of pew doors.

The Commissioners and Visitors appointed to purify the church in the Protectorate of Oliver Cromwell listed the Rev John Barton of Aylesbury a 'scandalous minister' and it was voted that he would be expelled.
On 8 July 1642 information in writing was given to the House of Commons that John Barton had spoken against the Parliament.
As a result, he was sent for and delivered to Parliament in custody of the Sergeant-at-Ar
In 1611 the Aylesbury Grammar School moved to what was then church buildings. These buildings now house the County Museum. The school remained here until 1907.
In 1622 the south-east pier underwent a second buttressing, and at perhaps some other period the casing was built round that to the north-east, and its arches walled up. This is proof that in one instance at least (that of the south-west pier) the second casing failed at an early date, as is shown by the large clamps which have been added to it. There have subsequently there been continued failures in casing of both of the western piers.
On Aylesbury Church there are no monuments from the 17th century or before and it did not at the time of its restoration in the 18th Century contain a single particle of ancient coloured glass. Therefore, the Church during this period is said to have undergone some exceedingly rough usage. During restoration work in the 19th Century they opened some of the closed archways prior to beginning work. Injuries to the building were to be observed inflicted on the ornamental stone work, which could not have been the result of accident. This damage was ascribed to the period of the English Civil War during the reign of King Charles I. Exposed as the Aylesbury district was to the full force of the mischievous effects of the civil commotions of that period, it would indeed have been extraordinary if this Church above all others had escaped the ravages and excesses of those unfortunate times, when the noblest ecclesiastical structures of our country were plundered, defamed, and defaced. Let us not forget the so-called Battle of Aylesbury on 1 November 1642. Indeed, in August, 1642, Nehemiah Wharton, a Parliamentarian soldier, writes from Aylesbury, telling his friends how they attacked a man called Penruddock, whom he called a Papist. He said the attack was because he had been "basely affronted by Penruddock and his dog". Finally he adds that he and his men "showed their zeal" and "got into the church, defaced the ancient and sacred glazed pictures, and burned the holy rails".
A description of the church says how there was an old gallery in the church with its bird-cage pew. This pew was completely enclosed with lattice work and its front was ornamented with filigree work, presenting the appearance of a box at the opera, and thus named the bird-cage. This was the old manor pew, and was occupied by the judges and High Sheriff at the Assize sermon, and used upon other state occasions. The church also had a pulpit at the front which was nicknamed by the congregation a 'three-decker'.
Some of the pews in the body of the church were fitted with brass rails and hangings to make them more private. In the north chapel were the high pews which were raised some feet above the floor and reached by three or four steps. The whole of the nave was filled with paneled pews over which the occupiers claimed exclusive and permanent right; it was thought something grand to be known as the owner of a 'faculty pew'. The divisions which were exceedingly high, were adorned according to the various owners; some were lined with blue cloth and bedizened with an abundance of large brass-headed nails; others would be scarlet; green baize was the prevailing 'comfort', whilst some of less pretensions were satisfied with paint. These pews were of all shapes and sizes, without the least pretense to uniformity. There was a jealous feeling respecting possession of pews; and it was a common practice for many of the owners to keep the doors carefully locked. When the wicked man came into church, his arrival was announced by the clicking of the locks of pew doors.
The Commissioners and Visitors appointed to purify the church in the Protectorate of Oliver Cromwell listed the Rev John Barton of Aylesbury a 'scandalous minister' and it was voted that he would be expelled. On 8 July 1642 information in writing was given to the House of Commons that John Barton had spoken against the Parliament. As a result, he was sent for and delivered to Parliament in custody of the Sergeant-at-Ar
St Mary the Virgin's Church, Aylesbury