On August 3, 1854, the State appointed Niernsee as architect, Niernsee examined Hammerskold's work and found it and the materials Hammerskold had used both defective and wholly unsuitable. The work was dismantled; the loss totaled $72,267.

On November 27, 1854, Governor John L. Manning recommended erecting a new State Capitol with north and south exposures at the intersection of Senate and Main (then Richardson) Streets. He thought that "If change of location be made, in the end perhaps it may not be a subject much to be regretted that delay and disaster attended the first efforts to construct a new Capitol for the commonwealth." The General Assembly acted on Governor Manning's recommendation, changed the site, and ordered a design with wings extending east and west.

Niernsee planned to complete the building in five years. By 1857, it rose to the top of the basement window-heads. On October 1, 1860, Niernsee reported that the structure had risen nearly sixty-six feet above the foot of the foundation and that the "absolute value of the work put into the building," was $1,240,063. The Corinthian granite capitols, some 64," he said, were "being executed in a style and finish heretofore unequalled in that line."

Work on the new State House was suspended when Sherman's army destroyed Columbia on February 17, 1865. Shells from Sherman's cannons, which were of light calibre, damaged the building only slightly, and brass markers were subsequently placed on the west and southwest walls of the building to show where the shots had landed. Ten were fired in all. Six "struck the western front," with little damage "except one which shattered the moulded windowsill and balusters of the 2d window (from the northern end) of the Hall of the House of Representatives." Four struck the interior of the building.

More devastating was the fire that destroyed the old State House. Niernsee reported it cracked five "bells of St. Michael's Church, Charleston," which had been "sent up here some time ago" and deposited under one of the sheds." It consumed the valuable State House library, offices, and workshops, a vast quantity of finished marble and rough material, estimated by Niernsee to be worth $700,000, and several thousand drawings, the result of his practice of twenty-five years. "These," said Niernsee, along with "one of the latest and best busts of Calhoun" and all the valuable detail State House drawings, contracts, and so forth, which had accumulated during Niernsee's ten years on the job, "were utterly swept away during that terrible night-an irreparable loss."

All that remained of Niernsee's drawings were several prints of a perspective view and one full-sized detail of a Corinthian capitol. This perspective and evidence in the building itself, however, indicate Niernsee's concept of the completed structure. His plan did not contemplate a dome that looked anything like the dome on today's building. His was a lofty and finely proportioned tower, which rose one hundred eighty feet from the ground through the center of the building supported by piers and arches; it was "a rectangular lantern," somewhat pyramidal in outline, and thirty feet square at the base; its projected cost was $200,000.

Niernsee returned to Columbia to resume his work as architect of the State House in 1885, but he died on June 7. He was succeeded by a former associate, J. Crawford Neilson, of Baltimore. On October 1, 1888, his son, Frank Niernsee, took over and worked largely on the interior until construction was again suspended, this time about 1891.

In 1900, Frank P. Milburn became architect. He hired the contracting firm of McIlvain and Unkefer, replaced the roof, and built the present dome and north and south porticos for about $170,000. Senator J. Q. Marshal of the State House Commission protested Milburn's appointment, however, and launched an investigation of the work. The investigation ended when the State brought suit against Milburn and his contractor, but the case ended in a mistrial and was not retried.

A joint legislative committee, after calling in Captain S.S.Hunt, the superintendent of construction of the United States Capitol, characterized the dome as infamous. "No uglier creation could be devised," it lamented, "and it is nothing short of a miserable fraud."

On April 8, 1904, the State elected Charles C. Wilson of Columbia as architect. Wilson worked on the terrace and steps of the north front and made sundry improvements to the interior. His work continued for several years and cost about $100,000.

Wilson, who admired Niernsee's design, described the style as "Roman Corinthian, with considerable freedom and distinguished originality in much of the detail. The workmanship of Maj. Niernsee's time," he said, "is exceptionally fine, indicating not only his great genius but the enthusiastic cooperation of mechanics of the highest skill and integrity. ...All credit for this noble and dignified building is due to the original designer and architect, Maj. John Niernsee. It is due him and to future generations of South Carolinians that it be protected from further departure from his design, and in good time, in the state's future prosperity, it is not too much to hope that it may yet be restored to his ideal."

Although all legislative records for the building are not available, those that are show the General Assembly appropriated at least $3,540,000 for its construction over the years. The granite for the structure, according to Alexander S. Salley, who wrote a history of the State House in the early-twentieth century, came mostly from the Granby quarry, which was located about two miles south of the State House.