The area suffered severe flooding in the late 14th century, leading to financial difficulties and a merger of the two vicarages from 1398 onwards.

It remained a parish church when the Abbey was dissolved and the rectory and advowson devolved to the Crown, who initially leased it to the widow Mary Blackenhall for 21 years in 1540.

In 1557 these were bought by Robert Thomas and Andrew Salter using money from the estate of William Pownsett of nearby Loxford, and granted to All Souls College, Oxford, in return for the vicar praying for the souls of Pownsett, his parents and benefactors every Sunday, giving 6 shillings and 8 pence amongst twenty poor people annually on the anniversary of Pownsett's death, paying the College an annual sum to maintain two poor scholars and only being absent from the parish 80 or fewer days a year.

The right is now shared between All Souls College, Oxford, the Bishop of Chelmsford (in whose diocese it now falls) and the church's churchwardens.

[9] In 2007, two small stones from remains of the old medieval London Bridge[10] were joined together in a sculpture in front of St Margaret's church facing the Barking Abbey ruins as part of several public artworks placed in Barking Town Centre by artist Joost Van Santen.