The important Holtgräve organ in the Lebuinus Church was built from 1836 till 1838. It incorporates many parts of the earlier organ. There is also a choir organ by Ankersmit (after 1940).

Albert Schweitzer, organist and Bach scholar, played the organ of this church on two occasions: 15 April 1928 and 12 May 1932. George Frederic Handel played here in 1750.

The grandfather of Sweelinck (called Swibbert van Keysersweert) and his brother (Gerrit Swybberts) were organist here. The father of Jan Pieterszoon moved to Amsterdam with his family when Jan Pieterszoon was still young. They are mentioned on a memorial tablet under the organ, which lists the organists of the church.