The most famous feature of St John the Baptist's Church is the array of well-preserved and ancient wall paintings in the nave and on the chancel arch.
 They are part of a series painted by monks from Lewes Priory; this was the first Cluniac house in England and had close links to its mother priory at Cluny in Burgundy, and the art techniques developed at Cluny from the mid-10th century were very influential.
 Murals from the same school—known as the Lewes Group—can also be seen at Coombes Church near Shoreham-by-Sea, St Botolph's Church at Hardham and St Michael and All Angels Church at Plumpton, and were once visible at the church in Westmeston as well.
 The examples at Clayton have been described as "some of the most important in the country", "remarkable", "a fine set", "amazing", "unique in England for their extent, preservation and date", and "graphically representing ... the terrors of Judgment Day".
 They are also some of the oldest surviving murals in England, although their age is not known for certain.
 Historians have variously dated them to the 11th century, c. 1080, between 1080 and 1120, c. 1100, "later than 1125", c. 1140, c. 1150 or late 12th century.

The murals cover the chancel arch and the east, south and north walls of the nave, and were uncovered between 1893 and 1895 when Charles Eamer Kempe was restoring the interior.
 More were uncovered during subsequent alterations between 1917 and 1919.
 Nikolaus Pevsner believed that the west wall would have had similar paintings as well.
 Most authorities agree that they are frescoes—painted directly on wet plaster.
 Like the other Lewes Group paintings, they feature a very small range of local pigments in shades of yellow and red (leading to the nickname "bacon-and-egg").

The main subject of the murals is the Day of Judgment, making them an early example of the "Doom" paintings seen in medieval churches across England.
 Pevsner noticed that the figures had characteristic features: "extremely long and lean, with heavy ... garments, exceedingly small heads ... [and] strange headgear".
 Centrally placed above the chancel arch is an image of Christ in Majesty in a mandorla held by angels and with apostles on each side.
 Flanking this are Christ giving the Keys of Heaven to Saint Peter (to the left) and a book to Saint Paul.
 On the north wall of the nave, a procession (led by bishops) approaches the Heavenly Jerusalem, watched by angels and saints, and the defeat of the Antichrist.
 Scenes on the south side include angels, one of the Four Horsemen of the Apocalypse, worshipping saints and another procession, this time of the damned: in this dramatic composition, "a spike-heeled devil riding a large beast separates the doomed from the blessed".
 An angel is also depicted at each corner of the nave: this is another reference to the Day of Judgment, when, according to the Gospel of Mark, "shall He send His angels, and shall gather together His elect from the four winds, from the uttermost part of the Earth to the uttermost part of Heaven" (Mark 13:27).
 The paintings are heavy with symbolism, and "give a full interpretation of the Last Judgment": in medieval times such paintings were the most important way of conveying information and narratives to worshippers, many of whom could not read.

In 2010, it was reported that the murals were threatened with damage from bat faeces.
 A colony of bats—a protected species—were roosting in the church, and church staff had to remove droppings from the walls before each service.
 Bat urine was also harming the timbers of the roof.
 A survey by specialists indicated that although the paintings were still "in good condition", their age and fragility increased the risk of damage.
The most famous feature of St John the Baptist's Church is the array of well-preserved and ancient wall paintings in the nave and on the chancel arch.  They are part of a series painted by monks from Lewes Priory; this was the first Cluniac house in England and had close links to its mother priory at Cluny in Burgundy, and the art techniques developed at Cluny from the mid-10th century were very influential.  Murals from the same school—known as the Lewes Group—can also be seen at Coombes Church near Shoreham-by-Sea, St Botolph's Church at Hardham and St Michael and All Angels Church at Plumpton, and were once visible at the church in Westmeston as well.  The examples at Clayton have been described as "some of the most important in the country", "remarkable", "a fine set", "amazing", "unique in England for their extent, preservation and date", and "graphically representing ... the terrors of Judgment Day".  They are also some of the oldest surviving murals in England, although their age is not known for certain.  Historians have variously dated them to the 11th century, c. 1080, between 1080 and 1120, c. 1100, "later than 1125", c. 1140, c. 1150 or late 12th century.
The murals cover the chancel arch and the east, south and north walls of the nave, and were uncovered between 1893 and 1895 when Charles Eamer Kempe was restoring the interior.  More were uncovered during subsequent alterations between 1917 and 1919.  Nikolaus Pevsner believed that the west wall would have had similar paintings as well.  Most authorities agree that they are frescoes—painted directly on wet plaster.  Like the other Lewes Group paintings, they feature a very small range of local pigments in shades of yellow and red (leading to the nickname "bacon-and-egg").
The main subject of the murals is the Day of Judgment, making them an early example of the "Doom" paintings seen in medieval churches across England.  Pevsner noticed that the figures had characteristic features: "extremely long and lean, with heavy ... garments, exceedingly small heads ... [and] strange headgear".  Centrally placed above the chancel arch is an image of Christ in Majesty in a mandorla held by angels and with apostles on each side.  Flanking this are Christ giving the Keys of Heaven to Saint Peter (to the left) and a book to Saint Paul.  On the north wall of the nave, a procession (led by bishops) approaches the Heavenly Jerusalem, watched by angels and saints, and the defeat of the Antichrist.  Scenes on the south side include angels, one of the Four Horsemen of the Apocalypse, worshipping saints and another procession, this time of the damned: in this dramatic composition, "a spike-heeled devil riding a large beast separates the doomed from the blessed".  An angel is also depicted at each corner of the nave: this is another reference to the Day of Judgment, when, according to the Gospel of Mark, "shall He send His angels, and shall gather together His elect from the four winds, from the uttermost part of the Earth to the uttermost part of Heaven" (Mark 13:27).  The paintings are heavy with symbolism, and "give a full interpretation of the Last Judgment": in medieval times such paintings were the most important way of conveying information and narratives to worshippers, many of whom could not read.
In 2010, it was reported that the murals were threatened with damage from bat faeces.  A colony of bats—a protected species—were roosting in the church, and church staff had to remove droppings from the walls before each service.  Bat urine was also harming the timbers of the roof.  A survey by specialists indicated that although the paintings were still "in good condition", their age and fragility increased the risk of damage.
St John the Baptist's Church, Clayton