[1]: 2 Between 1212 and 1222 the earlier structure became the church of the new St. Thomas college of Augustinian canons founded by Markgraf Dietrich von Meissen.

[1]: 2 In 1217, the minnesinger Heinrich von Morungen bequeathed to the church a relic of St. Thomas as he entered the order of canons after an apocryphal trip to India.

Following an inflow of wealth into Leipzig from the discovery of silver in the Ore Mountains (Erzgebirge), the Romanesque nave was demolished and replaced between 1482 and 1496 by the current late-Gothic hall church.

[1]: 2 The composer Johann Sebastian Bach was Thomaskantor, director of music, from 1723 until his death in 1750 and taught at its affiliated school.

[1]: 2 During the Nazi era, the church office worked with government officials to identify which congregants were of Sinti-Romani heritage, ultimately leading to the death of certain parishioners at concentration camps.

In the 20th century, sulfur emitted from nearby coal mines, and other pollutants in the atmosphere caused the deterioration of exterior stonework and statuary, and even of interior Gothic paintings.

It was moved to the new St. Paul Church in 2014 and replaced in 2016 with a Gothic-revival altar by Constantin Lipsius made in 1888, which had been removed in 1964.

[9] A statue of Felix Mendelssohn Bartholdy, who lived in Leipzig from 1835 until his death in 1847, was dedicated on 18 October 2008, when it was re-erected opposite the St. Thomas Church on the occasion of the year of his 200th birthday.

Celebratory speeches were given by Kurt Masur, also a former Gewandhaus Orchestra director, and Burkhard Jung, mayor of Leipzig.

[1]: 3 The church features a number of works of art, including a baptismal font (1614–15) made by Franz Döteber and Portraits show the Stadtsuperintendent of Leipzig, the oldest dating from 1614.

They show a number of historic motifs: a memorial to the fallen of World War I, King Gustavus Adolphus of Sweden, Johann Sebastian Bach, Martin Luther with Elector Friedrich der Weise and Philip Melanchthon as well as Emperor Wilhelm I.

In 1894, the anatomy professor Wilhelm His was commissioned to identify the composer's remains amongst disinterred bones from the cemetery where Bach had been buried.

He concluded that "the assumption that the bones of an elderly man, which had been found in an oak coffin near the Johanneskirche, were the remains of Johann Sebastian Bach" (translated from German) was very likely.

The new grave with a bronze cover (sponsored by the Leipzig cultural officer of the Soviet Army) was inaugurated on 28 July 1950, 200 years after the death of the composer, who is now buried in the sanctuary of the Thomaskirche.

To 1908 Sauer rebuilt and enlarged the organ after instructions from Karl Straube, it contains now pneumatic key action and 88 stops.

The German organ builder Christian Scheffler reconstructed and repaired the Sauer-organ in two phases: 1988 to 1993 and in the years to 2005.

It is headed by the Thomaskantor, an office that has been held by many well-known composers and musicians, including Johann Sebastian Bach from 1723 until his death in 1750.