In response to an appeal from the town, John Keeling, junior minister in Southampton, went up to Farnham in 1810 and preached. This led to the formation of a society, meeting in rented rooms and Farnham became a mission the following year. The Religious Census of 1851 recorded Methodists meeting in a house in Longbridge Street, with seating for 35. (There is also a record of Farnham Methodists walking to Hale on Sunday mornings for worship in a carpenter's shop, which was used until a chapel was built in Upper Hale in 1861.) The arrival of a butcher, John Swansborough, in 1877 led to a renewal of the Upper Hale society, with services being resumed in the chapel by 1884.
By 1864 the Farnham Wesleyans were meeting in a loft in Wheatsheaf Yard. Three years later they moved into an iron chapel seating 100 in Long Garden Walk. With the continuing growth of the town, in 1871 they built a more permanent church in South Street opened in December 1872, though not registered as a place of worship until 1875. The iron chapel, re-erected behind the church, continued in use as a Sunday School until replaced by a purpose-built schoolroom in 1878. In 1892 the church itself was refaced in stone, with gothic windows and the addition of a tower.
Meanwhile, in addition to the Upper Hale chapel, the Wesleyans also built one at Rowledge and one was built at Star Hill, Churt in 1883 by a local artist, James Clark Hook, was served by both Wesleyan and Bible Christian ministers.
The Bible Christians also had a Farnham Mission, which include Bats Corner, Crondall, Blacknest, Bramshot and later the Liphook Mission.
The Primitive Methodists opened a chapel at Badshot Lea in the 1860s, replaced in 1902 by a larger chapel south of the crossroads, on a site given by Richard Hyde, a Tongham sand and gravel merchant, and demolished in 1987. Their first meeting place in Farnham was a room in Long Garden Walk; followed by one in Downing Street. In 1878 they built a chapel seating 200 on the new Union Road which survived until after Methodist Union, but closed in 1936, the congregation moving to South Street church. Their chapel became part of the Co-operative Stores and was demolished in 1989.