The church is named for the Observantine Franciscans or "Grey Friars," who arrived in Edinburgh from the Netherlands in the mid-15th century and were granted land for a Catholic friary at the south-western edge of the burgh.

After its reconstruction, the minister, Robert Lee, introduced the first organ and stained glass windows in a Scottish parish church since the Reformation.

Notable features of the church include historic stained glass windows by James Ballantine; the 17th century monument to Margaret, Lady Yester; and an original copy of the National Covenant of 1638.

[3] The friary enjoyed royal patronage and connections: it hosted Mary of Guelders on her arrival in Edinburgh in 1449 and sheltered Henry VI of England during his exile.

This edict does not appear to have been enforced until 1598, when the south-west parish was allocated to the Upper Tolbooth partition at the west end of St Giles'.

In 1599, the town council had discussed and abandoned proposals to construct a new church in the grounds of Kirk o' Field (around modern-day Chambers Street).

Robert Traill, the covenanting minister of Greyfriars, was forced into exile and Covenanters were imprisoned in a field adjoining the kirkyard after the Battle of Bothwell Brig in 1679.

[27] The congregation met in the chapel of George Heriot's School and the "Lower Commonhall" of the University of Edinburgh while the church was repaired.

Hugh Miller unsuccessfully argued the congregations should move to St John's Church on Victoria Street and leave Greyfriars as a scenic ruin.

[29] The majority of the town council's members had joined the Free Church and their attempts to frustrate the restoration were one of the reasons it ended up taking twelve years.

[38] After the church reopened in 1857, Lee embarked upon what became known as "the Greyfriars Revolution": he introduced a service book of his own devising and pioneered the practices of standing for praise, kneeling for worship, and saying prepared prayers.

Since this union, Greyfriars has maintained the tradition of the Edinburgh's Highland congregation by hosting regular Gaelic language services.

[53] Until 1591, burials were restricted to the northern half of the site; the Upper Yard, where the Kirk now stands, was held by the magistrates and wapinschaws were conducted there.

Below the central window at the east end is a low, Renaissance-style semi-octagonal porch with a door in each of the three full faces and a pitched roof.

In that year, the town council also ordered the removal of the buttresses and doors of the Convent of Catherine of Siena at Sciennes for use in the construction of the new church.

[62][65] According to George Hay, the form of an aisled nave, while "exceptional" in post-Reformation Scotland, did not represent a step back to pre-Reformation practices.

[30] Galleries were then added to make up for lost space; the former north door was moved one bay east and its keystone was adorned with a carving of an angel's head; plaster ceilings, coombed in the aisles and barrel-vaulted over the nave, were raised.

In November 1719, the town council commissioned Alexander McGill to build a new church in the western half with Gilbert Smith as mason.

David Bryce designed new furnishings for New Greyfriars: a tall wainscot was installed and north, south, east galleries now faced a canopied pulpit at the west end.

The arcades were not reconstructed, leaving an open interior covered by a single-span timber ceiling beneath a steeply pitched roof.

[74] The current three-manual organ stands at the west end of the church and was built by Peter Collins of Melton Mowbray in 1989.

[76] Carved details on the cases by Derek Riley show Scottish plants and animals, a Franciscan Friar, and Greyfriars Bobby.

Along the frieze of the towers runs the penultimate phrase of Psalm 150: "Laudate Dominum onme quod spirat" ("Let everything that hath breath praise the Lord").

Other individuals commemorated by plaques in Greyfriars include Thomas Ruddiman, Robert Wallace, and Alexander Nisbet, and Walter Scott.

[87] The dais and oak wainscot and communion table at the east end of the church were added in 1912 to designs of Herbert Honeyman.

The wainscot, whose Canopy incorporates depictions of the wounds of Christ, was adorned by the addition of gilt cross to the central panel in 1963: this was donated by City of Edinburgh (Fortress) Royal Engineers.

[91][46][92] A U.S. flag hangs in the north aisle: this was given by the Consul General of the United States of America in 1970 to commemorate the 350th anniversaries of both the landing of the Pilgrims at Plymouth Rock and the opening of Greyfriars.

[42] Three ministers of Old Greyfriars were elected moderator of the General Assembly of the Church of Scotland during their incumbencies: George Kay in 1755,[98] William Robertson in 1763,[99] John Inglis in 1804.

New Greyfriars was especially active in mission work, using the Gaelic Chapel in Castle Wynd and, in 1846, founding the Vennel Ragged School: one of the first of its kind in Edinburgh.

Since the death of the Reverend Ewen Maclean in 2000, an ecumenical roster of ministers and preachers have led services; worship also features the unaccompanied singing of the Psalms.