[6] The cemetery was constructed during 1850, on plans laid out by Edward C. Jones, and included a Gothic chapel also designed by Jones which no longer exists.

[7] The chapel, which was located near the central lake, remained under construction until early 1851.

[8] Both the chapel and the porter's lodge sustained very heavy damage during the cemetery's occupation by federal forces during the Civil War.

[9][10] The porter's lodge at the entrance was demolished in 1868, but the chapel continued to be used until at least 1876.

[11][12] According to a 1909 newspaper account, "There is a rule in Charleston that colored people shall not be allowed to parade through Magnolia cemetery, the principal burying place of the white citizens," and this exclusion policy was enforced regardless of social status, such as in the case of Dr. Crum being prohibited from driving through the cemetery.