In 1381 Wat Tyler on his way to Smithfield to meet the king during the Peasants Revolt set fire to the church. The building was quickly rebuilt afterwards and continued to be used by the the order until the dissolution of monasteries. The dissolution in 1540 dissolved the order of St John and demolished all structures except the chancel.
After the destruction of the dissolution the church was used for secular use becoming an office, the Master of the Revels which licensed plays including those of Shakespeare. The building was however quickly reverted back to religious use as a chapel and in the early eighteenth century it is recorded as being a Presbyterian meeting house. In 1721 it was bought and was mostly rebuilt giving it much the appearance it has today. In the late nineteenth century at the church above was 'restored' by the Victorians taking out many Georgian additions. From the same restoration project the twelfth century under the chancel was restored and cleaned and converted into a chapel. The church became the parish church of St John for some years until 1921 when it was given to the new order of St John of Jerusalem who used it as their chapel. During the Second World War the church was badly bombed, by the end of the war it was left a blackened shell. The order of st John restored and rebuilt the church afterwards, although not to original designs. One new positive feature is the cloister garden built in the 1950's.
Unfortunately the church today is in my view a rather ugly mess of restoration and post war rebuilding. However, the twelfth century crypt (pictured left ©) survived the disasters inflicted on the church and is one of the most atmospheric and authentic medieval crypts in London and is well worth a visit. Another remnant of the priory church is St Johns gate which was originally the gateway to the priory. St Johns gate is just to south of the church on the road to Smithfield.
First Picture © showing church post-war plans for the church. More information including opening hours at http://www.museumstjohn.org.uk/your_visit/index.html