Whether due to his feelings about the war, or the lack of opportunities in Charleston, John Drayton soon left the Lowcountry and headed west. By the end of 1865, he joined his two brothers, who had survived the war, in Texas. In 1868, he was living across the border in Mexico. He never returned to Charleston.
Before he left, Dr. John set up the first contracts with several companies to mine phosphate at Drayton Hall. His nephew, Charles Henry Drayton, took over these contracts when he came of age and eventually started his own company, Charles H. Drayton & Co.
Charles H. Drayton & Co. operated from 1881 into the early 1900s. During that time, Charles Henry built a narrow gauge railroad, fifteen houses, and two stores at Drayton Hall to support the mining operation. He also converted the existing brick privy into an office and installed a fireplace. While Charles H. Drayton & Co. was in business, strip mining took place as close as 1,000 feet from the main house.
Profits generated by the phosphate mining operations allowed the Draytons to recover from the war. The walls, originally painted a creamy khaki color, were repainted in shades of blue. Wooden fish-scale shingles replaced brickwork in the pediments on both facades. A balustrade was extended across the upper portico. New machine-made balusters and Victorian newel posts completed the damaged staircase in the stair hall, and a new roof was added.
The Draytons also re-landscaped the property. Although the land-front lawn was the "working side" of the plantation in the 18th century, by the turn of the 20th century, it was no longer the gateway to rice fields. To reflect new styles, the family excavated part of the land-front lawn by an aged oak tree and diverted water from a former rice pond to create a reflecting pond and then used the spoils to create a three-tiered garden mound in front of the portico.