When Henry IV conquered the city of Erfurt, the churches were set on fire along with the people who had taken refuge in them.

Afterwards, the church known as the Hohes Münster ("High Minster") was demolished and rebuilt in a smaller form on the same site.

As a third institution on this site, Archbishop Adalbert of Mainz (1109–1137) had an episcopal residence built before 1123, the Krummhaus ("Crooked House") to the east of St Severus' Church.

As space became increasingly scarce, Adalbert moved the Benedictine nunnery of St Paul to the Cyriaksberg in 1123.

The documentary evidence for the building is extraordinarily fortunate, as numerous indulgences were granted that report on the progress of construction.

Some reports already refer to the first repairs after a lightning strike in 1327, which also killed several people, suggesting that the church was already being used again at that time.

The large number of donations of altars, vicars and widely known High-Gothic sculptures indicates Erfurt's economic rise at this time.

In the 1370s and 1380s, there were several disputes, some of them physical, between the two capitularies over the single-storey, two-bay Blaise's Chapel built on the south side between 1358 and 1363 and the boundary between the two churches, which were not settled amicably until 1387.

However, a second side aisle was added to the north and south, giving the entire church the width of the transepts, which thus no longer protruded outwards.

The huge hipped roof covering the entire nave (1472–1473) and the present shape of the eastern end with its three-steeple group date from this period.

The choir side towers, square in plan, originally date from the High Gothic period, but they were destroyed except for the lower storeys and then rebuilt, taking on their present form with slender spires in 1495.

The raised central tower with the bell storey was probably also added at this time, and the pointed spire is dated 1494.

The west choir was demolished together with the connections for the cloister, and a two-storey extension with a Cross chapel was built in its place by 1495.

The late Gothic Virgin Mary altar (1510) in the northern side aisle is attributed to the Saalfeld School.

The figures of saints on the side wings are carved in flat relief and show St Ursula (with arrow and book) and Mary Magdalene (with ointment jar).

After the fire of 1472, an ambitus was built on the west side of the church and in front of the southwest corner, perhaps only restoring an older state without profound changes.

In 1485, a new sacristy (demolished in 1818) and a capitular hall were built on the north side of the church, and ten years later a new cloister was completed.

In 1633, St Severus' Church was occupied by Swedish troops and subsequently handed over to the Protestants, who altered the interior by demolishing an altar and relocating the pulpit.

The relics that came to Erfurt in 836 under Archbishop Otgar of Mainz were of such great significance that the monastery was renamed "St. Severi".

When the church was rebuilt, it became necessary to redesign the tomb, which continued to be placed in a central position, presumably near the west choir.

The almost fully sculptural high reliefs depict scenes from the life and work of Saint Severus and the Adoration of the Three Magi, based on a model in Nuremberg's Church of St Lawrence from 1360.

The Catholic Boniface's Chapel is a square tower, still Romanesque in parts, which may originally have belonged to the archbishop's castle.