The Nineteenth Century
The Church was again in poor state of repair and unable to cope with the number of worshippers in a growing town. In 1823 a plan was prepared by the Reverend W.F. Baylay to build a larger new Church on the site of the old one. A meeting was held to discuss the plan and after opposition from some parishioners, it was decided to retain the old Church and to provide a new Church with its own parish elsewhere in the town. The parish of Holy Trinity was formed when a new Church was consecrated in 1825. As the town of Margate expanded in the 19th century, further new Churches and parishes were established: St. Paul's, St. James, St. Saviour's and All Saints. Several daughter Churches were also established to serve the more distant parts of the parish.

A major restoration of the Church building took place in 1875 and a good deal of the present appearance of St. John's is the work of the Victorians. The architect was Ewan Christian who was responsible for restoring more than twenty Kent Churches.
The galleries and box pews were removed and new teak pews were installed.

The floor was lowered and the old lead covered roof was removed. A new trussed rafter pine roof was built and tiled. The original flintwork of the tower was revealed when the stucco was chipped off. The low spire was also removed and the fine shingled broach spire was erected in its place.
The timbers for the new spire were fashioned a short distance away at Paramor's Yard, now a part of the Dreamland Amusement site.
The Victorians were also responsible for installing stained glass windows and a new organ.
The Churchyard was extended several times and the Tudor vicarage which faced Victoria Road was demolished in 1836 to create additional burial space which as needed until the town's cemetery opened in 1853. There was a tithe barn on the site of the Community Centre and ancient cottages which had once been used by Church candle makers stood in the Churchyard opposite the South Door.