There is no surviving record of when the first Methodist society was formed in Bungay, but a chapel was opened in October 1802 in Neatgate Street (now Chaucer Road). It was still burdened with debt in 1831, but in 1836 a new chapel of local white bricks was built in Trinity Street, opposite Cross Street.

The return for the 1851 Religious Census recorded 350 sittings, with a morning congregation of 32 plus 20 Sunday School scholars, 60 plus 12 scholars in the afternoon and 40 in the evening. There were 42 members in the society at that time. The evening congregations reported in the various churches was unusually small because of a memorial service in the Corn Hall for four men accidentally killed, attended by over 1,000 people.

In 1900 the Trinity Street church underwent major alterations and had seating for 250.

Originally in the Norwich Circuit, Bungay Circuit was formed in 1809. It was always a small one and almost always in debt. The Quarterly Meeting consistently refuses to authorize ministers' removal and medical expenses and occasionally refused travelling expenses for attending Conference. The circuit was renamed Beccles Circuit in 1890. By December 1930 Bungay was in the Beccles Section of the Lowestoft Wesleyan Circuit.

It is not clear when the Primitive Methodists first missioned the town. However, the Religious Census recorded in 1851 that a chapel with 134 sittings had been built the previous year. Attendances were 140 in the morning, 159 in the afternoon, with just 33 in the evening (presumably because of the memorial service). The chapel did not survive long, and in 1856 the Corn Hall was rented for a short time while they looked for somewhere cheaper. At this time Bungay was a Mission in the Norwich First Circuit.

A chapel was built in 1862 on Bardolph Road, constructed of clay lump with brick footings. In 1864 the Norwich First Circuit offered Bungay to the Yarmouth Circuit, but it was declined because of an outstanding debt. The creditor, Samuel Jarrold of Norwich, agreed to take the chapel in lieu of payment and continued to be a benefactor to the congregation, paying among other things for a young preacher to live at Bungay.

By 1896 the Primitive Methodists were meeting in a chapel in South End Road. When the circuit boundaries were rearranged in 1906, Bungay was included in the Lowestoft and Beccles Primitive Methodist Circuit. In 1908 a new chapel was built on Laburnum Road, constructed in red and yellow brick with a slate roof and seating 180.

At Methodist Union in 1932, the Wesleyan and Primitive Methodist congregations united. The former PM building was considered unsafe; it was closed and sold in 1933 and demolished in the 1940s. On 17 November 1940 the Trinity Street chapel was badly damaged by a bomb exploding nearby. Further damaged was caused in another raid in 1942. The schoolrooms in the basement were used for worship until government grants were secured and building licences obtained, The building was repaired by the Norwich architect Clifford Dann and reopened in September 1948.

By 1966 the society was included in the Beccles, Bungay and Loddon Circuit. Then in 1976 the congregation joined with the United Reformed Church to become Emmanuel Church. The Trinity Street church was sold to the Bungay Branch of the St. John's Ambulance Brigade and is now used as auction rooms.