The beginnings of the Stellwagen organ north wall of the church, date back to 1467. The late Gothic façade, which has been preserved to the present day, housed a Gothic block organ, which was extended into a three-manual organ in 1637 by the organ builder Friedrich Stellwagen.

Stellwagen added a few stops to the former block organ (now the Hauptwerk), built a Brustwerk underneath it and installed a Rückpositiv in the gallery balustrade. The pedal action was located behind the Hauptwerk. Before and after this extension, the organ was under the shadow of the large organ of the church. As a result, we are fortunate today that only a few alterations were carried out in the meantime, so that the historical material has been largely preserved.

In 1931 Hugo Distler was appointed to the Jakobi Church and in 1935 he initiated a restoration of the organ.

Fortunately the instrument was saved from the destruction of the Second World War.

In 1977/78 a thorough restoration of the instrument was carried out in accordance with the rules of monument conservation. Restoration by the company Gebrüder Hillebrand from Altwarmbüchen near Hannover.

It is one of the few organs in the world where an original stock of Gothic and Renaissance pipework has been preserved.