There are many churches in Aberdeen, in the town itself and also in Thembalesizwe and Lotusville.
In the centre of the town is the NGK (Dutch Reformed Church), with its impressive spire that some say is the tallest in the country at a little over 50m. The church was completed in 1907 and is constructed in the Cape Gothic tradition.Coming into Aberdeen from Graaff-Reinet one can see a slight “lean”of the spire to the left, due to the weight of the roof tiles added onto the wooden framework. On the west side of the church grounds there is an olive tree that was grown from a slip taken from the Garden of Gethsemane.

The oldest church building in the town is the Methodist church, on the corner of Grey Street and Brand Street. The foundation stone was laid in 1882, and the church was eventually opened at the end of 1883. It is a simple, stone built, rectangular building, with Gothic buttresses and arched windows. Unusually, the bell tower is topped with a belfry of cast iron lacework.

Also in town are the Afrikaanse Protestante Kerk, the Apostolic Faith Mission and St Mary and All Saints Anglican Church.