Lady Yester funded the completion of the Tron and gave money for the church that would bear her name.

During this period, the church was not used for regular worship; though laureations (graduations) of the nearby town college were held here.

That year, the town council commissioned two Huguenot furniture makers, Paul Roumieu senior and Peter Pittit, to repair the church.

[11] From 1687, the congregation of Holyrood Abbey occupied the church following their displacement from their place of worship by James VII.

That year, Lady Yester's parish was reinstated and Thomas Wilkie of the Tolbooth was appointed minister.

To fill this, the town council used its right of patronage to appoint John Drysdale against the wishes of the General Sessions, which usually elected ministers to the burgh churches.

The Court of Session and House of Lords both found Drysdale's presentation was valid and he was inducted to the charge on 24 August 1764.

The controversy saw several members leave Lady Yester's and form Edinburgh's first Relief congregation, which eventually settled nearby at South College Street.

Noted for his schemes to extract profits as beadle of Lady Yester's and as doorman to the General Assembly, he was caricatured by John Kay with the caption "Prayers at All Prices".

The school was established in response to an appeal by the Presbytery of Edinburgh, issued after a riot on New Year's Day 1812, during which a murder was committed and three boys were executed.

[22] Following Fleming's death, the town council imposed John Lee as minister against the wishes of the congregation, who had requested the services of Robert Gordon.

[25] During the early 19th century, noted physician John Abercrombie worshipped at the church, as did the bookseller David Laing.

[19] Bennie introduced private tuition for children, which was formalised as a Congregational School shortly after his death in 1846.

[30] In 1859, the addition to the parish of a portion of St Leonard's between St Leonard's Lane and Brown Street was proposed but never advanced; the following year, management of Edinburgh's burgh churches, including Lady Yester's, passed from the city council to the city's Ecclesiastical Commissioners.

[31] By this time, city improvements were massively altering the southern part of the Old Town and Chambers Street was cut through Lady Yester's parish, depleting the area's population and the church's congregation.

[33] The church and hall were sold to the city council who, in turn, gave them to the University of Edinburgh's for the use of the Works Department.

[35] Until the erection of St Mary's, Bellevue in 1824, Lady Yester's and New Greyfriars were the only two of the eight burgh churches to have one minister rather than two.

[44] Prior to her death, Lady Yester ordered the addition of an aisle to the church, which would go on to serve as the place of her burial.

[48][49] This was surrounded by boundary walls and only accessible via a gate at High School Wynd (now Infirmary Street).

The façade, in ashlar, consists of a Dutch gable facade of three bays with short pinnacles on the corners.

[51][52] Sibbald's plan also included detached pavilions on either side of the church, facing onto Infirmary Street.

[8] This was moved to the west wall of the lobby of the second church then to Greyfriars Kirk following Lady Yester's secularisation.

The central panel is framed by two Renaissance pillars and features at its top a skull and crossbones below an hourglass, wings, and blades of corn in relief.

This motif is surrounded by a banderole bearing the mottoes "MORS PATET HORA LATET" ("death is sure, the hour is hid") at the top and "SPES ALTERA VITÆ" ("hope of another life").

[56] Lady Yester's brass First World War memorial plaque is also mounted on the wall of this aisle.