 Woodruff was elected three times as Lieutenant Governor of New York and served from 1897 to 1902.In the process Woodruff became the only Lieutenant Governor in New York history to serve under three different Governors — Frank S. Black, Theodore Roosevelt, and Benjamin Barker Odell, Jr. As Lieutenant Governor, Woodruff took a leadership role in the Association for the Protection of the Adirondacks, helping to protect the forests there from the devastation of clear cutting and large scale damming projects.In 1904, Woodruff's wife Cora died.