During the years of 1861- 1865, the city of New Orleans suffered greatly. The congregation at St. Paul continued to worship and serve the community. After the Civil War in 1866, St. Paul began providing support for many orphans in the city, and organized a Sunday school and in 1881, the congregation was able to support the start of an orphanage.
On February 5, 1889, St. Paul Church burned down again to the foundation. The building was rebuilt and rededicated on September 15, 1889; and has been in use ever since.