In the 17th century the south transept appears to have burnt down, and was not restored until the Rev Peter Aubertin rebuilt it in 1855, using the north transept as his model.
In the 18th century the church was served from Croydon. It is related that the dead used to be brought to the church and left until the parson next came round! The church appeared to be held in rather low esteem and suffered a long period of neglect with cricket matches held on Church Green and the church used as a pavilion for refreshments. The Rector would announce the next meet of the hounds from the pulpit. The coming of the Rev'd Peter Aubertin and his son changed all that and their influence was paramount.
The Rev'd Peter Aubertin, of Huguenot stock, came to St Margaret's as curate and restored the old Rectory at Mugswell for his use. He became Rector in 1808 and began a long period of alterations and improvements to the church starting in 1827. A new organ was installed in 1852. His son initiated a programme of major structural changes to the church in 1882 which were finally completed after his death in 1889. These changes transformed the appearance of the church and included the rebuilding of the north wall to create the north aisle for additional seating, and the installation of the present pews. This was the great age of Victorian 'restorations', and while great improvements were achieved, some of the historic details of the old church were inevitably lost.
The expense of the restoration work was borne through the generosity of Mr J G Cattley of the Shabden estate. In return, Mr Cattley was granted exclusive use of the north transept for 'the owners and occupiers of the Shabden Estate'. This arrangement continued until the death of Lord Marshall in 1936.
By 1900 the Rev'd Charles Young found the Rectory at Mugswell too far from the church and let it, finding lodgings in the village. In 1902 the new Rector, James Hervey, moved into the new Rectory in Elmore Road, an arrangement which continued until 1989 when the Rectory was sold to release funds to the Diocese. Rev John Gooden moved into the present Rectory in Starrock Lane in 1990.