In 1129 Norbert von Xanten (1080/85–1134), Archbishop of Magdeburg since 1126, handed over the abbey to the reformed order of Premonstratensians, which he himself had founded in Prémontré, France, in 1121. The community lived in a strict interpretation of the rules of St. Augustine. When Norbert von Xanten died in 1134, he was interred in front of the rood altar. A few years later his remains were transferred to the convent chancel, which at this time presumably extended far into the crossing, or even westwards beyond it. Shortly after being taken over by the Premonstratensians a period of great construction activity began. It was at this time that the church received its distinctive western end with the bell tower in the width of the nave, flanked by slender round towers. Shortly after this the portal was erected on the south side of the church, which was to have its counterpart opposite. Even more importantly, around the middle of the 12th century the columns were replaced by piers, with only the first pair of columns to the west of the crossing pier remaining. A fire in the city in 1188 also damaged St. Marien although – contrary to what was previously assumed – recent structural research shows that this had no great impact on the architecture of the church.

Parallel to the reworking of the church, the cloister with two-storey “tonsure” was erected. Another addition in the mid-12th century was the so-called “high-columned chapel” to the north of the choir, used as a sacristy in the 16th century and perhaps already intended for this purpose, as well as the north wing with the barrel-vaulted refectory and cellar – a second one beneath it dates from the late medieval period.

In the west wing the piers in the southern hall, open to the cloister, were replaced by slender columns - in part from re-used materials. Tombs in the floor, wall painting and stained-glass windows, all of which are only known from 19th century depictions and archaeological excavations in the 1930s, suggest that the room, which was destroyed by aerial bombardment in the second world war, was the chapter house. In the 17th century the room, known colloquially as the “cowling”, was regularly used for meetings of the Landstände, predecessor to the present-day state parliament. Since reconstruction this has been the location of a museum café. The northern hall was divided up in the course of the medieval period.
The two-storey barrel vault must have been erected at an angle to the northern transept and the nave before the cloister; the lower level once housed an altar, whilst the upper level is referred to as “poenitentiarium”, a room for detention. At that time, the inner cloister also included a kitchen to the west of the refectory (used as such until 1945, now the museum foyer) and a dormitory projecting eastward as an extension of the south wing.

The next significant architectural intervention for the church came in 1225/30 with the installation of the early Gothic vault, still in situ today, ascending to a gangway beneath the clerestory windows in the nave and the transept. The roof above dates largely from the year 1310.

The Magdeburg Premonstratensian chapter was now officially the leading abbey of the religious order in Saxony, whose provost, “Secundus Primas Germaniae” within the order from 1224 onwards, was responsible for a total of sixteen Premonstratensian chapters, including the cathedral chapters of Brandenburg, Havelberg and Ratzeburg. After extensive dispute, in 1295 the chapter general in Prémontré permitted the provosts of the Magdeburg abbey and its filiations to gather at the tomb of the founder of the order every three years on the anniversary of Norbert’s death and that only one of them was required to travel to Prémontré.

The Premonstratensians also assumed a prominent role within the city itself, when in 1349 Archbishop Otto von Hessen transferred the patronage of the Magdeburg church of Sankt-Ulrich-und-Levin, which also signified patronage of all other churches within the city. In addition, they were also patrons of the parish churches at Burg and Schönebeck, for example.

Numerous buildings belonging to the monastery were located in the direct vicinity of the cloister. Around 1400, for example, the monastery received a new provost’s building in front of what is now the museum entrance. A spital dedicated to St. Alexius once stood to the south-west of the tower façade, whilst a guest house was erected to the east of the choir in the early 16th century (a rose bed is now located above the still-intact cellar). To the south of the church stood an Alexius and an Ölberg chapel. Following their demolition in 1888 the façade was placed to the north of the refectory. Very little of all this remains, as the area around the monastery was rebuilt several times from the 18th century onwards before being destroyed in the second world war, with the remnants subsequently cleared, with the exception of a few walls.
Also no longer present is the dormitory, which was renewed after a fire in 1445 and renovated following war damage in 1550/51; heavily damaged again in 1631, it was demolished completely in the mid-19th century.

Construction work to the church is not documented again until the early 16th century, when the choir was modernised with the addition of new windows and a new apsis arch.

In 1591 the Magdeburg Marienkirche became operational once again – with a Protestant church service led by Dean Siegfried Sack. Here too, the Reformation was now unstoppable; following the death of Adam Helfenstein in 1597, who had held the office of provost since 1589, Adam Löder (in office 1597–1612) became the first Protestant provost. The last Catholic conventuals left the monastery in 1601, with the establishment continuing to be used until 1834 as a Protestant and subsequently secular facility, 1698 to 1945 as a boarding school, from 1928 combined with the Protestant cathedral grammar school.
It was only in the years 1628 to 1632 that a Catholic Premonstratensian convent returned to the monastery in Magdeburg. When it was forced to leave the city with the destruction of Magdeburg, in addition to the library it also removed the entire archives, a gap that has still not yet succeeded in being filled.

Shortly after Norbert’s canonisation the Premonstratensians were already making efforts to retrieve the bones of the order founder from the primarily Protestant environment. However, this attempt did not come to fruition until 1626 with the support of the emperor, with the bones subsequently being transferred to Strahov Monastery, in Prague.
At that time the interior of the church looked very different to today. When Norbert’s bones were retrieved, the head section of his still-existing stone coffin was located in the rood altar that adjoins the convent choir to the west, whilst the remainder of the coffin, visible from the western crypt, lay beneath the floor of the choir, raised up eight steps from the transept. However, it is unclear when the room, the dimensions of which were only revealed again in the course of recent renovations, to the west of the 11th century choir crypt was constructed; at the time of Norbert’s exhumation at least there was not yet an altar here. The pilaster strips on the walls, excavated in 1976, suggest construction in the last quarter of the 16th century, after Norbert’s canonisation; however, this barely matches the oldest description of the tomb, dating from precisely this time, hinting at an older origin. In any case, the pilaster strips form part of a two-aisled layout of the room. Prior to this a three-aisled space must have adjoined the eastern Werner crypt, although the size of this can no longer be reconstructed due to the later conversion work carried out.

Today, the coffin of St. Norbert is integrated as a relic into an altar standing at the height of the western crossing pier in the front crypt area. Above the head section the late-Gothic altar plate of secondary use displays a niche, with the missing coffin lid providing a direct view of the empty coffin. This altar was presumably erected by the Premonstratensians that returned to Magdeburg again in1628, it is known that the extensive damage caused by the opening of the tomb in 1626 gave them reason to begin conversion work within the church, probably resulting in a reduction of the choir in the area to the east of the crossing. However, this work was not completed prior to their departure, it was not until 1638 that the crossing crypt was enclosed with a timber ceiling, rendering the Marienkirche, which had suffered relatively minor damage during the storming and destruction of Magdeburg in 1631, ready for use for church services again.

Although the school used the church, in around 1700 Provost Philipp Müller (in office 1679-1702) ordered comprehensive renovations, however, it was not assigned a parish of its own. In 1689 religious refugees from Alsace held their church services here for a while, and in the 18th century it served as a Protestant garrison church.

During the Napoleonic Wars the Marienkirche was used as a warehouse, a field hospital and to house livestock, with furnishings and fabric of the building suffering greatly as a result. After this, from 1819, by royal decree, it became home to the Catholic congregation of Magdeburg, having grown again, who had the church comprehensively restored. After their relocation to St. Sebastianskirche, St. Marien stood empty once again, with the school having been secularised in the meantime. 1890/91 the church was restored again in the Romanesque style, after which church services were held here again regularly.
1925/26 saw the renovation of the cloister, followed by the west wing in 1934. The Old Lutheran congregation met in St. Marien. Severe damage in the second world war was suffered by nearly all buildings in the area of the outer cloister, together with the west wing of the cloister, part of the east wing and the vault beneath the church choir. In 1947 work began on the reconstruction of the church, which resulted in its purification. The Old Lutherans were now using other areas of the cloister, with the Reformed congregation using the church from 1953 to 1971. A boarding school was established in the former school area, whilst a school for children with speech defects was housed in parts of the cloister until into the 1980s.