In 1849 the large congregation again divided, with most of its white members leaving to form the Fredericksburg Baptist Church at Princess Anne and Amelia Streets.

Services were discontinued during the American Civil War, and the existing building was damaged, in part due to abuse caused during military occupation of the city.

However, due to a schism in the congregation, two separate groups claimed the name "Shiloh Baptist", which was resolved by giving the one at this location the name "Shiloh Baptist Church (Old Site)", which it still retains.

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