It remained in this form until it was demolished, making it one of the very few churches in Erfurt that did not undergo any major structural changes, either as a result of city fires or due to dilapidation.

After Erfurt was defortified in 1872, the Löbervorstadt district moved southwards, whereupon numerous new residential buildings were erected between the Flutgraben ditch and the Steigerwald forest from 1890 onwards, and the Old St Thomas' Church no longer offered enough space for the growing congregation.

After the groundbreaking for the New St Thomas' Church on 29 April 1900, work began on a new neo-Gothic building in a park on Schillerstraße street under the direction of the pastor Alfred Fritzsche and the Hanoverian architect Rudolph Eberhard Hillebrand.

In return, the old St Thomas' Church was demolished a year later and previously, valuable furnishings, such as the altar retable from 1445 and a sacrament house, were taken over into the new building.

Explosive bombs hit the eastern nave of St Thomas' Church and severely damaged the roof and the outer wall in this area.

Internal USAAF reports later revealed that this air raid had originally been intended for the town of Gotha and that, due to poor visibility on that day, a target confusion had taken place.

Despite adverse conditions, St Thomas' Church could be rebuilt according to designs by the architects Theo Kellner and Karl Tetzner under the supervision of the pastors Kurt Pohl and Johannes Mebus and was re-consecrated on 24 September 1950.

In 1947 and 1956, coloured glass windows were installed, which had been manufactured by the workshop of Ernst Kraus in Weimar according to designs by the graphic artist Karl Völker from Halle an der Saale.

On 15 March 1957, four new steel bells were delivered from the Schilling foundry in Apolda and named Christus, Thomas, Luther and Menius by Bishop Johannes Jänicke from Magdeburg on 29 September.

In 1974, twelve bronze relief plates for the door of the main portal were donated by the pastors Johannes Mebus and Kurt Pohl and cast according to the designs of the Berlin sculptor Werner Stötzer.

During the time of the GDR, the church was in permanent decay due to the persistent lack of building materials, so that the roof was in a very poor condition by the early 1980s.

In January 2000, St Thomas' Church was renovated by the architectural firm of Hardt, Scheler und Partner and in the process, the 4.5-metre-high (14 ft 9 in) rose window on the north wall, which had been bricked up in 1945, was restored and fitted with new glazing based on designs by Susanne Precht from Lauscha.

The door of the main portal is divided into twelve sections, each of which is decorated with a bronze relief plate designed by Werner Stötzer and depicting various scenes from the life of the apostle Thomas.

On the north wall of the eastern gallery hangs a sculpture of Christ nailed to a cross, created by the Erfurt artist Hans Walter in 1952.

Before the Second World War, St Thomas' Church had a large organ built by the Eberhard Friedrich Walcker organ-building workshop in Ludwigsburg with 74 sounding stops on four manuals and pedal, which was, however, destroyed by a bombing raid on Holy Saturday 1945.