Lyman returned to Boston and joined the firm of
Ropes, Gray, Boyden & Perkins. His nomination was confirmed by the United States Senate five days later. On March 4, he resigned from the Republican National Committee, as he did not want his duties as collector and committeeman to conflict with each other. He took office on April 1. Lyman's administration as collector was described by A. Maurice Low of
The Boston Daily Globe as having been "managed in the interest of both the government and the merchants doing business with the customhouse, and that there has been practically no friction." He was nominated for reappointment as collector of customs by President
Theodore Roosevelt on January 8, 1902. In February 1902,
The Boston Daily Globe reported that Massachusetts Governor
Winthrop M. Crane and others suggested to President Roosevelt that Lyman would be an able successor to
United States Secretary of the Navy John Davis Long. Roosevelt and Lyman were friends, and Roosevelt respected Lyman's abilities as a businessman and his record as collector. On April 2, 1906, Lyman was sworn in for an unprecedented third term as collector. He was promised reappointment to a fourth term but chose to retire instead, citing "personal reasons". In 1918, the director of the Massachusetts Committee on Public Safety
Henry Bradford Endicott appointed Lyman to chair a subcommittee of the Public Safety Committee to supervise groups that made public appeals for funds for patriotic purposes. The committee was formed to root out duplication of services, inefficiency, wastefulness, and dishonesty in patriotic societies. It was created soon after an organization known as "The Chain" began soliciting funds in Boston. The Chain's purported treasurer denied any involvement with organization's and Endicott believed its list of patrons was suspect as well. Lyman later wrote a book about the history of the Massachusetts Committee on Public Safety. ==Personal life==