Although the town of Wisbech has evidence of Saxon settlement, the church of St Peter & St Paul is Norman in origin. Traditionally said to have been founded in the year 1111, the evidence tends to suggest a slightly later date for the first church building, possibly somewhere around 1150. The church sat on a spit of land, sandwiched between the river estuary (the town was then on the southern edge of the Wash) and the Norman castle moat.

The first Norman church was probably a small building with a single nave and a western tower separated from the nave by a heavy arch, the foundations of which can still be seen at the western end of the main nave.

By 1250 the growing prosperity and population of the town was reflected in the extension of the church but the site, hard up against the castle moat, limited room for expansion to the west. Instead, the apse at the eastern end of the nave was demolished and a widened chancel built – the resulting “crank” between the two is still evident today although this could have been intended to be temporary until the rest of the Norman building could be demolished. The original outer walls were removed to the north and south and a second nave was created along with a side aisle to the south. By 1400 the reconstruction had created the basic form that exists today and also one of only two parish churches in the UK with a double nave covered by a single roof.

At some point during the 1400s a storm caused the tower to collapse into the building, no doubt causing serious damage to the surrounding structure. The southern side of the Norman nave was dismantled and replaced with a high perpendicular range of arches between the two naves. A new tower was completed by about 1530, standing slightly apart from the main building to the north. At about the same time, a chapel had also been built alongside the chancel and the southern porch had been constructed. From the reign of Queen Elizabeth 1 to the Victorian period, little was changed other than internal fittings. A medieval rood screen between nave and chancel was removed, leaving scars on the pillars that remain and undoubtedly much decoration was removed during the Reformation and the Commonwealth periods. In 1663 Samuel Pepys visited the town and noted "..a fine church and library, where sundry very old abbey manuscripts; and a fine house, built on the church ground by Secretary Thurlow, and a fine gallery built for him in the church". Eventually by the early 1700s seven heavy overhead galleries had been constructed and tall box pews were installed. At this stage, the church would probably have become very gloomy inside with much of the natural light obscured. During the later Victorian period, the church was restored under the direction of Sir Gilbert Scott. This work saw the removal of the galleries that were creating damaging stress on the structure and the old box pews thereby restoring the interior to more or less its Elizabethan appearance. The coloured glass is almost all Victorian, with the exception of some 15th century fragments high in the sanctuary wall. During the late 20th century restoration has continued and more pews have been removed to create a more flexible space. The overcrowded graveyard that surrounded the church was transformed into gardens and now forms the venue for the annual Rose Fair. The need to fund repairs to the tower in the 1960s prompted the first Rose Fair. Within the building there are many notable features, including a full size brass effigy of Sir Thomas de Braunstone, the constable of Wisbech Castle who died in 1401. There are also fine 17th and 18th century memorials in the chancel and a magnificent Royal Coat of Arms dating from the 1660’s. A memorial was dedicated in 1985 to the Far East Prisoners of War of 1939-45, many of whom came from Wisbech and Cambridgeshire, captured at the fall of Singapore. The church organ is among the finest in the UK. Built in 1951 by Harrison & Harrison to replace an earlier instrument dating from 1787, the organ was reconditioned and modernised in the 1990s by Richard Bower & Co. The tower contains the 3rd oldest full peal of 10 bells in the world, cast by William Dobson in 1821. Some of the bells were recast from an earlier 8-bell peal, the oldest bell dating from 1566.