The war, however, proved detrimental to the company's fortunes. The Confederate government ordered railroad companies to send rolling stock to other companies that transported the most troops and military goods/equipment. The need for passenger service increased as well and this reduced the demand for freight service. The company was able to make profits on passenger service but maintenance of tracks was difficult because they were being constantly used. Additionally, the ravages of the war itself as well as General Sherman's March to the Sea destroyed the company's tracks and cars, amounting to 140 miles of track, 14 locomotives, and 97 cars.
The company rebounded from the war and started to make profits again from freight service in 1867. It repaired destroyed rail lines and added 1,500 more miles of track. The company started to use diesel steam engines in the 1940s but maintaining and repairing them in the shops at the complex proved to be unsuitable. As a result, the company gradually shifted operations to Macon. In 1963, the Southern Railway Company bought Central of Georgia and finally closed all operations at the complex. The museum opened in 1989 and is operated by the Coastal Heritage Society.