The Romanesque St Martin’s Kirk is estimated to have been built in the 1150s, near the start of Scotland’s current parochial division system. It belonged to the Cistercian Nunnery of St Mary’s, which was founded by Ada, Countess of Northumberland and wife of Prince Henry of Scotland. Used by both nuns and common folk, the kirk was one of Haddington’s main houses of worship and is now the only part of Countess Ada’s project still standing.

It's thought that Haddington native John Knox attended this church during his childhood. Knox, ordained as a Catholic priest, grew to become one of the key figures in the 16th century Scottish Reformation, which advocated for Protestantism. The 1560 attack that caused St Martin’s roof to collapse is likely to have been organized by Knox in what some see as a possible act of retribution.

A number of mysteries have given St Martin’s ruin a reputation as an architectural oddity. For starters, conflicting sources mean that it has not yet been fully determined if the church was built before the nunnery or vice-versa. That only the church’s walls still stand make a definitive answer unlikely. A 13th-century expansion of the church indicates that what is now the arched entry to the ruin was originally a chancel arch, though experts have been unable to identify some key chancel arch characteristics.

Finally, a series of square openings line all four walls of the church. While these are commonly caused by ceiling-supporting wooden beams decomposing, St Martin’s are larger and closer together than most other wooden beam “putlog” holes. If they were indeed left behind by wooden beams, it has not yet been fully determined why these were bigger and closer to each other than those of contemporary buildings.