About a century later a stone church was built on to the tower, of which the doorway and font remain. The font was originally square, however the corners were cut off in the 15th century in line with the prevailing octagonal style.

A larger building replaced the Norman church in the 14th century. The nave of this is still intact, however it has since been enriched with 15th century woodwork and window tracery. The Rood screen dates from 1490, and is decorated with Angels of the Passion at the base.

In 1705, the Church of St Andrew in the neighbouring village of Flixton was destroyed in a gale. It was never repaired, and the ruins can still be seen today. Therefore, in 1724 the two parishes were joined into one, officially called St. Mary the Virgin, Blundeston, with St. Andrew, Flixton. The original font from Flixton now stands in St. Mary's churchyard, and there is an altar dedicated to St. Andrew inside the church.

The pews, all in oak, date from the 1850's when the church was extensively restored, and are a rare example of Victorians being sensitive to medieval work, as they fitted them to the surviving 14th century poppy heads nearest the wall. The ceiling is an example of late Victorian barrel-vault, which rests on 14th century corbels in the form of kings and queens.

Today, the Church of England parish of Blundeston with Flixton shares a rector with the four members of the Somerleyton Group of Parishes (Somerleyton, Ashby, Fritton, Heringfleet), and St. John the Baptist, Lound. The building also hosts services for the local Methodist church.