Two things governed changes in parish churches ­ then as now ­ fashion and money. The new large windows inserted in the 14th century would have lit an interior rich in colour, the walls painted, the glass itself probably stained, and the pictures providing a comprehensible illustration to a largely illiterate population. A rood screen would have separated the chancel, which was the priest's church, from the nave, which was the people's church. The huge wooden screen with a large crucifix (the rood), maybe flanked by the Virgin Mary and St John, would have dominated the interior in the 15th and early 16th centuries, the only remnant now being the base, stencilled with simple coloured flowers. Many rood screens had a loft, accessed by a small winding stair (which in the case of the church in Little Thurlow is only 15´´ wide), from which musicians played their instruments.

Edward VI (b 1537­ d 1553) decreed that such decorations should be removed, so images were torn down and the rood screens were dismantled, although some were re-instated when Mary, a staunch Catholic, came to the throne in 1553. Her reign was short, and Elizabeth I acceded to the throne in 1558, decreeing that England should become a stable Protestant nation. She wanted a standard religion, and indeed the version of her Prayer book (originally printed in six languages by John Daye of Little Bradley) is still used today. The damage to the interior decoration of the churches had been done, the vibrant colours were painted over and much of the ornate carving disappeared.

Further desecration took place during the Puritan uprising in 1649 when Cromwell strove to remove all signs of idolatry from the church. The church became a preaching house with the emphasis on the pulpit, not the altar, and pews were introduced with the most ornate pews for the members of the big house. St Peter's is a good example, with the large box pew in the chancel. The Soame family enlarged the church to accommodate the enormous memorial to Sir Stephen Soame, which comprises recumbent alabaster effigies of Sir Stephen and his wife and the kneeling figures of his family. It is likely that the family also inserted the clerestory windows and the altar rails during the 1600s.

In common with countless other country churches, the present interior owes more to the Victorians than any other age and was 'new pewed ' in 1843 when the choir stalls were installed. The oak pulpit is dated 1876 and probably replaced a much more ornate affair, although the brass chandelier is much earlier and dates from 1720, as does the 18th century sundial on the south face of the tower.