The Zuiderkerkstoren has a long and rich history. The pseudo-basilica was designed by city architect Hendrick de Keyser (1561-1632) and was built between 1603 and 1611. In 1614 the tower was finished, the tower contains the oldest bell (1511) of Amsterdam.

The gables on the north and south sides of the tower are designed in the Amsterdam Renaissance style, this is the signature style of Hendrick de Keyser. Other famous designs by Hendrick de Keyser are the Westerkerk, Noorderkerk and the mausoleum of Willem van Oranje in the Nieuwe Kerk in Delft. Hendrick de Keyser was interred in the Zuiderkerk after his death in 1621.

Three of Rembrandts (1606-1669) children are buried in the Zuiderkerk, which is located near his home in the Jodenbreestraat. Ferdinand Bol (1616-1680), a student of Rembrandt, was also buried in the church.

During his visit to the Netherland (presumably in 1874) French painter Claude Monet (1840-1926) made his famous painting of the tower. The painting is now located in the Philadelphia Museum of Art.

The Zuiderkerk was the first church in Amsterdam that was built for the protestant worship service. It held its first service on the day of Pentecost in 1611. In 1929 the Zuiderkerk lost its religious function as a result of a decline in visitors and the depopulation of the city center. The church became a storage centre and served as a morgue for the casualties of the war during the Dutch famine of 1944-45.

In 1968 the church became property of the municipality of Amsterdam. Starting in 1988 the church would be used as an information centre for spatial planning and housing. Since 2010 the church can be rented out for private and business events.