In 1658, on the bottom floor of the tower, a church is built. However, it is not consecrated until 1708. As Gamla Älvsborg is demolished in 1671, and its church ceases to exist, a number of oil portraits are moved to Nya Älvsborg, today decorating the handrail to the seating area. They depict the Savior, Moses, Jesaja, Jeremia, Hezekiel, Daniel and the evangelists. Jesus Christ on the cross is situated on the altarpiece. Above the altarpiece hangs a copy of a portrait of Karl XII. A unique placement some might think, especially in a church. The original portrait, in a golden frame, can be found in the Museum of Gothenburg as of 1917.

The last gathering here at Nya Älvsborg, with its congregation, is held on the 18th of April 1869. On the 14th of June 1871, His Royal Majesty decides the church of Nya Älvsborg is to become a part of the Lundby congregation, and that its inventory and treasury is to be surrendered to them. In the old church of Lundby you can now find the chandelier from Nya Älvsborg. The church here at Nya Älvsborg is one of the best preserved churches from the reign of King Karl XII. During Tordenskiölds second attack in 1719, a bullet came flying through the church window during assembly, piercing a leg of a soldier, and gets jammed in the wall. The bullet is still there today.