The church is a Gothic building made of brick, single-aisle, with a single tower on its axis, a stellar vault, a presbytery and a side chapel. It was built in 1417, on the site of the chapel by the hospital for the poor. In 1547, due to the building of fortification, the church cemetery was liquidated, and the main entrance to the church was bricked up.

With the Reformation spreading in Gdańsk and the Catholic churches being taken over by Protestant communities, St. Elisabeth’s Church was converted to the new denomination. Remaining in the hands of the hospital foundation, in the 16^th Century it constituted a place where ceremonies were organised for the Calvinist Scots and Netherlanders who served in the Gdańsk armies as paid soldiers.

In the same church, after five centuries, and serving Prussian soldiers as a garrison church from the mid 19^th Century, there were Masses for the soldiers of the allied occupation forces, stationed in Gdańsk between the end of World War I and the establishing of the Free City of Gdańsk.

At the turn of April 1945, the church, together with the church hospital, was burned down by the Red Army soldiers. The church was rebuilt by the Pallottine priests.

In October 1956 permission was granted to rebuild the old hospital, which, from then on, has functioned as a pastoral house. After renovation in 1993, the church acquired its present-day interior furnishing.

There is a story related to St. Elisabeth’s Church and the neighbouring St. Joseph’s Church, which is a manifestation of ecumenism and proof of tolerance for the cultural diversity present in the Gdańsk of those times. When, in 1678, the Carmelites’ monastery and St. Joseph’s Church were plundered during the riots, the monks found shelter in the Calvinist St. Elizabeth’s Church. To commemorate this event and express their gratitude for the impartial and interdenominational support for the Carmelites, the bells of St. Joseph’s Church have tolled each time the Calvinist priest from St. Elisabeth’s Church has died.