The origins of St Marien are closely linked to the development of the city of Lübeck. There was already a market church around 1160, shortly after the city was founded on its current site. It was initially the sole parish church of the city. Nobody knows today what it looked like. It was probably made of wood.

Lübeck became an episcopal city in 1160. When the first cathedral was consecrated in 1163, St Marien was placed under the jurisdiction of the canons. Early on, the city council fought for a say. St Marien remained the church of the leading citizens and the council, even after the other parishes were founded.

At the beginning of the 13th century, St Marien was a Romanesque basilica.

In 1251, rebuilding began in the style of a Gothic cathedral. Initially a hall church was planned, but then a high Gothic basilica with enormous dimensions was realised. The vaults span the impressive central nave at a height of 38.5 metres and the two towers reach 125 metres.

They were modelled on the great French cathedrals, above all those of Reims and Soissons. However, this meant that the Lübeck master builders had to reinvent the Gothic style to a certain extent. There were no quarries worth mentioning in the north German plain. The mighty, towering forms of the Gothic style had to be realised here with small bricks fired from clay.

At the beginning of the 14th century, the burghers and the bishop were in constant dispute. The fact that the citizens of Lübeck had the confidence to build a church out of brick that was larger than the nearby cathedral shows how self-confident and wealthy these citizens were in the 13th and 14th centuries.

The Reformation came late to Lübeck. Johannes Fritze, chaplain at St Marien, was one of the first preachers to publicly declare his support for the new movement from 1523. The canons removed him from his position and he went to Hamburg. However, the Protestant movement of the citizens could not be suppressed. This resulted in a so-called "singing war", in which Catholic masses were interrupted by the loud singing of Reformation psalm songs. The council and cathedral chapter were forced to revoke the dismissal of the popular Protestant chaplain Johannes Walhoff at St Marien at the end of 1529. In 1530, the Reformation prevailed in Lübeck with Johannes Bugenhagen's church order. This also led to a much greater involvement of the citizens in the government of the city.

The Reformation changed the interior of St Marien, but not violently as in other regions.

Not all, but many images and figures were removed: the statues of the Virgin Mary in the choir and the many images that adorned the Epistle Chapel. The most visible evidence of the Reformation was the new pulpit from 1534, which was decorated with elaborate reliefs and Low German sayings. Church services and sermons were now only held in the nave and choir and no longer, as before, in the many side chapels with their side altars. Despite the discontinuation of Marian worship, the church retained its name.

In the 17th and 18th centuries, the townspeople modelled their St Marien on Baroque ideals as far as the building allowed. The walls were whitewashed and a myriad of splendidly designed epitaphs of leading citizens hung from the pillars of the naves. They earned St Marien the slightly mocking title "Hall of Fame of the Lübeck Patriciate".

The close connection between the Council and St Marien began to loosen in the 18th century. In the 19th century, some of the baroque furnishings fell victim to the newly awakened appreciation of medieval art.

Soon after the National Socialists came to power, the city's Senate brought the Lübeck Evangelical Lutheran Church into line and disempowered the church councils - including that of St Marien. In 1934, the National Socialist Erwin Balzer was appointed bishop. St Marien was his official preaching church. St Marien's pastor Johannes Pautke, who belonged to the oppositional Confessing Church, was temporarily removed from office between 1936 and 1937, but was able to return after fierce protests.

On the night of 28-29 March 1942, Palm Sunday, British bombers attacked Lübeck. It was the first attack on a German historic city centre. St Marien was badly damaged. Parts of the vaults of the nave and aisle collapsed, as did the roofs of the towers.

The bells of the south tower fell and destroyed the medieval window panes, which were stored there in crates. The old organs were burnt. The medieval inventory of the church was almost completely destroyed.